Commit 1ed5edc8 authored by emarti2's avatar emarti2
Browse files

Metrics computation improvements

parent 31180b32
......@@ -23,11 +23,11 @@ nanosatellite,"accurate characterization of expanded tandem repeat length and se
Dynamic time warping of Oxford Nanopore squiggle data to characterize tandem repeats.
Several tools exist to analyze tandem repeats (e.g. tandem-genotypes and RepeatHMM)",[],[],"[{'term': 'DNA polymorphism', 'uri': 'http://edamontology.org/topic_2885'}, {'term': 'Sequence composition, complexity and repeats', 'uri': 'http://edamontology.org/topic_0157'}, {'term': 'Whole genome sequencing', 'uri': 'http://edamontology.org/topic_3673'}, {'term': 'Sequence sites, features and motifs', 'uri': 'http://edamontology.org/topic_0160'}]",[],1,[],False,False,[],[],[],[],[],[],MIT,False,False,['Kristel Sleegers'],[]
tricolor,Command-line application for tandem repeats profiling from error-prone long-read sequencing data.,['1.0'],['Bioinformatics portal'],"[{'term': 'Sequence composition, complexity and repeats', 'uri': 'http://edamontology.org/topic_0157'}]","[{'url': 'https://github.com/davidebolo1993/TRiCoLOR', 'note': None, 'type': ['Repository']}]",0,"[['Source code', 'https://github.com/davidebolo1993/TRiCoLOR']]",False,False,['https://github.com/davidebolo1993/TRiCoLOR'],['Linux'],"[{'data': {'term': 'nucleic acid sequence', 'uri': 'http://edamontology.org/data_2977'}, 'format': {'term': 'fasta', 'uri': 'http://edamontology.org/format_1929'}}]","[{'data': {'term': 'nucleic acid sequence', 'uri': 'http://edamontology.org/data_2977'}, 'format': {'term': 'fasta', 'uri': 'http://edamontology.org/format_1929'}}]",[],"[[['User manual'], 'https://davidebolo1993.github.io/tricolordoc/']]",GPL-3.0,False,False,['Davide Bolognini'],['https://github.com/davidebolo1993/TRiCoLOR']
tricolor,Command-line application for tandem repeats profiling from error-prone long-read sequencing data.,['1.0'],['Bioinformatics portal'],"[{'term': 'Sequence composition, complexity and repeats', 'uri': 'http://edamontology.org/topic_0157'}]","[{'url': 'https://github.com/davidebolo1993/TRiCoLOR', 'note': None, 'type': ['Repository']}]",0,"[['Source code', 'https://github.com/davidebolo1993/TRiCoLOR']]",True,False,['https://github.com/davidebolo1993/TRiCoLOR'],['Linux'],"[{'data': {'term': 'nucleic acid sequence', 'uri': 'http://edamontology.org/data_2977'}, 'format': {'term': 'fasta', 'uri': 'http://edamontology.org/format_1929'}}]","[{'data': {'term': 'nucleic acid sequence', 'uri': 'http://edamontology.org/data_2977'}, 'format': {'term': 'fasta', 'uri': 'http://edamontology.org/format_1929'}}]",[],"[[['User manual'], 'https://davidebolo1993.github.io/tricolordoc/']]",GPL-3.0,False,False,['Davide Bolognini'],['https://github.com/davidebolo1993/TRiCoLOR']
repet,"The REPET package integrates bioinformatics pipelines dedicated to detecte, annotate and analyse transposable elements (TEs) in genomic sequences. The main pipelines are (i) TEdenovo, which search for interspersed repeats, build consensus sequences and classify them according to TE features, and (ii)
TEannot, which mines a genome with a library of TE sequences, for instance the one produced by the TEdenovo pipeline, to provide TE annotations exported into GFF3 files.",['v3.0'],['Command-line tool'],"[{'term': 'Sequence composition, complexity and repeats', 'uri': 'http://edamontology.org/topic_0157'}, {'term': 'DNA', 'uri': 'http://edamontology.org/topic_0654'}, {'term': 'Nucleic acid structure analysis', 'uri': 'http://edamontology.org/topic_0097'}]","[{'url': 'https://urgi.versailles.inra.fr/download/repet/', 'note': None, 'type': ['Repository']}]",5,"[['Source code', 'https://urgi.versailles.inra.fr/download/repet/REPET_linux-x64-3.0.tar.gz']]",False,False,['https://urgi.versailles.inra.fr/download/repet/REPET_linux-x64-3.0.tar.gz'],"['Linux', 'Mac']","[{'data': {'term': 'dna sequence', 'uri': 'http://edamontology.org/data_3494'}, 'format': {'term': 'fasta', 'uri': 'http://edamontology.org/format_1929'}}]","[{'data': {'term': 'dna sequence', 'uri': 'http://edamontology.org/data_3494'}, 'format': {'term': 'fasta', 'uri': 'http://edamontology.org/format_1929'}}]",[],"[[['General'], 'https://urgi.versailles.inra.fr/Tools/REPET'], [['Installation instructions'], 'https://urgi.versailles.inra.fr/Tools/REPET/INSTALL'], [['User manual'], 'https://urgi.versailles.inra.fr/Tools/REPET/TEdenovo-tuto'], [['Training material'], 'https://biosphere.france-bioinformatique.fr/wikia2/index.php/REPET_practical_course_urgi']]",CECILL-2.0,False,False,['URGI'],['https://urgi.versailles.inra.fr/download/repet/']
kmasker,"Kmasker plants is a tool for the automatic detection of sequence regions with meaningful k-mer characteristics. This can be sequences with highly abundant k-mer patterns (repeats), regions with diverging k-mer patterns between two studied WGS samples or segments with high target specificity.","['1.1', '1.1']","['Command-line tool', 'Web service']","[{'term': 'Plant biology', 'uri': 'http://edamontology.org/topic_0780'}, {'term': 'Sequence composition, complexity and repeats', 'uri': 'http://edamontology.org/topic_0157'}, {'term': 'Nucleic acid sites, features and motifs', 'uri': 'http://edamontology.org/topic_3511'}, {'term': 'Comparative genomics', 'uri': 'http://edamontology.org/topic_0797'}]","[{'url': 'https://github.com/tschmutzer/kmasker', 'note': 'Source Code Repository', 'type': ['Repository']}, {'url': 'https://github.com/tschmutzer/kmasker/issues', 'note': None, 'type': ['Issue tracker']}]",1,"[['Software package', 'https://github.com/tschmutzer/kmasker/releases/download/1.1.0/kmasker_release.zip'], ['Software package', 'https://github.com/tschmutzer/kmasker/releases/download/1.1.0/kmasker_release_source.tar'], ['Downloads page', 'https://github.com/tschmutzer/kmasker/releases'], ['Software package', 'https://github.com/tschmutzer/kmasker/releases/download/1.1.1/kmasker_release.zip'], ['Software package', 'https://github.com/tschmutzer/kmasker/releases/download/1.1.1/kmasker_release_source.tar']]",False,False,[],"['Linux', 'Mac']","[{'data': {'term': 'dna sequence', 'uri': 'http://edamontology.org/data_3494'}, 'format': {'term': 'fasta', 'uri': 'http://edamontology.org/format_1929'}}]","[{'data': {'term': 'dna sequence', 'uri': 'http://edamontology.org/data_3494'}, 'format': {'term': 'fasta', 'uri': 'http://edamontology.org/format_1929'}}]",[],"[[['User manual'], 'https://github.com/tschmutzer/kmasker/blob/master/README.md'], [['Installation instructions'], 'https://github.com/tschmutzer/kmasker/blob/master/INSTALL.md']]",GPL-3.0,False,False,"['Thomas Schmutzer', 'Chris Ulpinnis', 'IPK-Gatersleben Research Group Bioinformatics and Information Technology', 'Sebastian Beier', 'Markus Schwalbe']",['https://github.com/tschmutzer/kmasker']
kmasker,"Kmasker plants is a tool for the automatic detection of sequence regions with meaningful k-mer characteristics. This can be sequences with highly abundant k-mer patterns (repeats), regions with diverging k-mer patterns between two studied WGS samples or segments with high target specificity.","['1.1', '1.1']","['Command-line tool', 'Web service']","[{'term': 'Plant biology', 'uri': 'http://edamontology.org/topic_0780'}, {'term': 'Sequence composition, complexity and repeats', 'uri': 'http://edamontology.org/topic_0157'}, {'term': 'Nucleic acid sites, features and motifs', 'uri': 'http://edamontology.org/topic_3511'}, {'term': 'Comparative genomics', 'uri': 'http://edamontology.org/topic_0797'}]","[{'url': 'https://github.com/tschmutzer/kmasker', 'note': 'Source Code Repository', 'type': ['Repository']}, {'url': 'https://github.com/tschmutzer/kmasker/issues', 'note': None, 'type': ['Issue tracker']}]",1,"[['Software package', 'https://github.com/tschmutzer/kmasker/releases/download/1.1.0/kmasker_release.zip'], ['Software package', 'https://github.com/tschmutzer/kmasker/releases/download/1.1.0/kmasker_release_source.tar'], ['Downloads page', 'https://github.com/tschmutzer/kmasker/releases'], ['Software package', 'https://github.com/tschmutzer/kmasker/releases/download/1.1.1/kmasker_release.zip'], ['Software package', 'https://github.com/tschmutzer/kmasker/releases/download/1.1.1/kmasker_release_source.tar']]",False,False,[],"['Linux', 'Mac']","[{'data': {'term': 'dna sequence', 'uri': 'http://edamontology.org/data_3494'}, 'format': {'term': 'fasta', 'uri': 'http://edamontology.org/format_1929'}}]","[{'data': {'term': 'dna sequence', 'uri': 'http://edamontology.org/data_3494'}, 'format': {'term': 'fasta', 'uri': 'http://edamontology.org/format_1929'}}]",[],"[[['User manual'], 'https://github.com/tschmutzer/kmasker/blob/master/README.md'], [['Installation instructions'], 'https://github.com/tschmutzer/kmasker/blob/master/INSTALL.md']]",GPL-3.0,False,False,"['Thomas Schmutzer', 'Chris Ulpinnis', 'IPK-Gatersleben Research Group Bioinformatics and Information Technology', 'Sebastian Beier', 'Markus Schwalbe']",['https://github.com/tschmutzer/kmasker']
TEannot, which mines a genome with a library of TE sequences, for instance the one produced by the TEdenovo pipeline, to provide TE annotations exported into GFF3 files.",['v3.0'],['Command-line tool'],"[{'term': 'Sequence composition, complexity and repeats', 'uri': 'http://edamontology.org/topic_0157'}, {'term': 'DNA', 'uri': 'http://edamontology.org/topic_0654'}, {'term': 'Nucleic acid structure analysis', 'uri': 'http://edamontology.org/topic_0097'}]","[{'url': 'https://urgi.versailles.inra.fr/download/repet/', 'note': None, 'type': ['Repository']}]",5,"[['Source code', 'https://urgi.versailles.inra.fr/download/repet/REPET_linux-x64-3.0.tar.gz']]",True,False,['https://urgi.versailles.inra.fr/download/repet/REPET_linux-x64-3.0.tar.gz'],"['Linux', 'Mac']","[{'data': {'term': 'dna sequence', 'uri': 'http://edamontology.org/data_3494'}, 'format': {'term': 'fasta', 'uri': 'http://edamontology.org/format_1929'}}]","[{'data': {'term': 'dna sequence', 'uri': 'http://edamontology.org/data_3494'}, 'format': {'term': 'fasta', 'uri': 'http://edamontology.org/format_1929'}}]",[],"[[['General'], 'https://urgi.versailles.inra.fr/Tools/REPET'], [['Installation instructions'], 'https://urgi.versailles.inra.fr/Tools/REPET/INSTALL'], [['User manual'], 'https://urgi.versailles.inra.fr/Tools/REPET/TEdenovo-tuto'], [['Training material'], 'https://biosphere.france-bioinformatique.fr/wikia2/index.php/REPET_practical_course_urgi']]",CECILL-2.0,False,False,['URGI'],['https://urgi.versailles.inra.fr/download/repet/']
kmasker,"Kmasker plants is a tool for the automatic detection of sequence regions with meaningful k-mer characteristics. This can be sequences with highly abundant k-mer patterns (repeats), regions with diverging k-mer patterns between two studied WGS samples or segments with high target specificity.","['1.1', '1.1']","['Command-line tool', 'Web service']","[{'term': 'Plant biology', 'uri': 'http://edamontology.org/topic_0780'}, {'term': 'Sequence composition, complexity and repeats', 'uri': 'http://edamontology.org/topic_0157'}, {'term': 'Nucleic acid sites, features and motifs', 'uri': 'http://edamontology.org/topic_3511'}, {'term': 'Comparative genomics', 'uri': 'http://edamontology.org/topic_0797'}]","[{'url': 'https://github.com/tschmutzer/kmasker', 'note': 'Source Code Repository', 'type': ['Repository']}, {'url': 'https://github.com/tschmutzer/kmasker/issues', 'note': None, 'type': ['Issue tracker']}]",1,"[['Software package', 'https://github.com/tschmutzer/kmasker/releases/download/1.1.0/kmasker_release.zip'], ['Software package', 'https://github.com/tschmutzer/kmasker/releases/download/1.1.0/kmasker_release_source.tar'], ['Downloads page', 'https://github.com/tschmutzer/kmasker/releases'], ['Software package', 'https://github.com/tschmutzer/kmasker/releases/download/1.1.1/kmasker_release.zip'], ['Software package', 'https://github.com/tschmutzer/kmasker/releases/download/1.1.1/kmasker_release_source.tar']]",True,False,[],"['Linux', 'Mac']","[{'data': {'term': 'dna sequence', 'uri': 'http://edamontology.org/data_3494'}, 'format': {'term': 'fasta', 'uri': 'http://edamontology.org/format_1929'}}]","[{'data': {'term': 'dna sequence', 'uri': 'http://edamontology.org/data_3494'}, 'format': {'term': 'fasta', 'uri': 'http://edamontology.org/format_1929'}}]",[],"[[['User manual'], 'https://github.com/tschmutzer/kmasker/blob/master/README.md'], [['Installation instructions'], 'https://github.com/tschmutzer/kmasker/blob/master/INSTALL.md']]",GPL-3.0,False,False,"['Thomas Schmutzer', 'Chris Ulpinnis', 'IPK-Gatersleben Research Group Bioinformatics and Information Technology', 'Sebastian Beier', 'Markus Schwalbe']",['https://github.com/tschmutzer/kmasker']
kmasker,"Kmasker plants is a tool for the automatic detection of sequence regions with meaningful k-mer characteristics. This can be sequences with highly abundant k-mer patterns (repeats), regions with diverging k-mer patterns between two studied WGS samples or segments with high target specificity.","['1.1', '1.1']","['Command-line tool', 'Web service']","[{'term': 'Plant biology', 'uri': 'http://edamontology.org/topic_0780'}, {'term': 'Sequence composition, complexity and repeats', 'uri': 'http://edamontology.org/topic_0157'}, {'term': 'Nucleic acid sites, features and motifs', 'uri': 'http://edamontology.org/topic_3511'}, {'term': 'Comparative genomics', 'uri': 'http://edamontology.org/topic_0797'}]","[{'url': 'https://github.com/tschmutzer/kmasker', 'note': 'Source Code Repository', 'type': ['Repository']}, {'url': 'https://github.com/tschmutzer/kmasker/issues', 'note': None, 'type': ['Issue tracker']}]",1,"[['Software package', 'https://github.com/tschmutzer/kmasker/releases/download/1.1.0/kmasker_release.zip'], ['Software package', 'https://github.com/tschmutzer/kmasker/releases/download/1.1.0/kmasker_release_source.tar'], ['Downloads page', 'https://github.com/tschmutzer/kmasker/releases'], ['Software package', 'https://github.com/tschmutzer/kmasker/releases/download/1.1.1/kmasker_release.zip'], ['Software package', 'https://github.com/tschmutzer/kmasker/releases/download/1.1.1/kmasker_release_source.tar']]",True,False,[],"['Linux', 'Mac']","[{'data': {'term': 'dna sequence', 'uri': 'http://edamontology.org/data_3494'}, 'format': {'term': 'fasta', 'uri': 'http://edamontology.org/format_1929'}}]","[{'data': {'term': 'dna sequence', 'uri': 'http://edamontology.org/data_3494'}, 'format': {'term': 'fasta', 'uri': 'http://edamontology.org/format_1929'}}]",[],"[[['User manual'], 'https://github.com/tschmutzer/kmasker/blob/master/README.md'], [['Installation instructions'], 'https://github.com/tschmutzer/kmasker/blob/master/INSTALL.md']]",GPL-3.0,False,False,"['Thomas Schmutzer', 'Chris Ulpinnis', 'IPK-Gatersleben Research Group Bioinformatics and Information Technology', 'Sebastian Beier', 'Markus Schwalbe']",['https://github.com/tschmutzer/kmasker']
ostrfpd,"Multifunctional Tool for Genome-Wide Short Tandem Repeat Analysis for DNA, Transcripts, and Amino Acid Sequences with Integrated Primer Designer.",[],"['Command-line tool', 'Desktop application']","[{'term': 'DNA polymorphism', 'uri': 'http://edamontology.org/topic_2885'}, {'term': 'Probes and primers', 'uri': 'http://edamontology.org/topic_0632'}, {'term': 'Sequence composition, complexity and repeats', 'uri': 'http://edamontology.org/topic_0157'}]",[],1,[],False,False,[],"['Linux', 'Windows', 'Mac']",[],[],[],"[[['General'], 'https://github.com/vivekmathema/OSTRFPD/blob/master/README.md']]",GPL-3.0,False,False,['Mallika Imwong'],[]
ultra,"> MEDIUM CONFIDENCE! | A Model Based Tool to Detect Tandem Repeats | ULTRA Locates Tandemly Repetitive Areas | To contribute to ULTRA development, you want to be on the develop branch, which is where we are currently integrating feature branches. For more information, see the ULTRA wiki",[],[],"[{'term': 'DNA polymorphism', 'uri': 'http://edamontology.org/topic_2885'}, {'term': 'Sequence composition, complexity and repeats', 'uri': 'http://edamontology.org/topic_0157'}, {'term': 'Transcription factors and regulatory sites', 'uri': 'http://edamontology.org/topic_0749'}]","[{'url': 'https://github.com/TravisWheelerLab/ULTRA/issues', 'note': None, 'type': ['Issue tracker']}]",1,[],False,False,[],"['Linux', 'Windows', 'Mac']",[],[],[],"[[['General'], 'https://github.com/TravisWheelerLab/ULTRA/blob/master/README.md']]",BSD-3-Clause,False,False,['Daniel Olson'],[]
pipealign2,"Takes one or more protein sequences as input and analyzes them in a five-step process during which searches for sequence homologues, analyses of multiple sequence alignments, and hierarchical relationships between protein subfamilies are performed.",[],['Web application'],"[{'term': 'Proteins', 'uri': 'http://edamontology.org/topic_0078'}, {'term': 'Sequence analysis', 'uri': 'http://edamontology.org/topic_0080'}, {'term': 'Protein sites, features and motifs', 'uri': 'http://edamontology.org/topic_3510'}, {'term': 'Sequence composition, complexity and repeats', 'uri': 'http://edamontology.org/topic_0157'}, {'term': 'Sequencing', 'uri': 'http://edamontology.org/topic_3168'}]",[],7,[],False,False,[],"['Linux', 'Windows', 'Mac']",[],[],[],[],Unlicense,False,False,[],[]
......@@ -78,15 +78,15 @@ remus,REinforced Merging techniques for Unique peptide Segments (ReMus) is desig
protparam,"Compute various physical and chemical parameters for a given protein sequence. The computed parameters include the molecular weight, theoretical pI (isoelectric point), amino acid composition, atomic composition, extinction coefficient, estimated half-life, instability index, aliphatic index and grand average of hydropathicity (GRAVY).",[],['Web application'],"[{'term': 'Small molecules', 'uri': 'http://edamontology.org/topic_0154'}, {'term': 'Sequence composition, complexity and repeats', 'uri': 'http://edamontology.org/topic_0157'}, {'term': 'Proteins', 'uri': 'http://edamontology.org/topic_0078'}, {'term': 'Computational biology', 'uri': 'http://edamontology.org/topic_3307'}, {'term': 'Proteomics', 'uri': 'http://edamontology.org/topic_0121'}, {'term': 'Sequence analysis', 'uri': 'http://edamontology.org/topic_0080'}, {'term': 'Function analysis', 'uri': 'http://edamontology.org/topic_1775'}]",[],1,[],False,False,[],"['Linux', 'Windows', 'Mac']",[],[],[],"[[['General'], 'https://web.expasy.org/protparam/protparam-doc.html']]",,False,False,"['SIB Swiss Institute of Bioinformatics', 'ProtParam Contact Form']",[]
prorepeat,An integrated curated repository and analysis platform or research on biological characteristics of amino acid tandem repeats.,[],['Database portal'],"[{'term': 'Sequence composition, complexity and repeats', 'uri': 'http://edamontology.org/topic_0157'}, {'term': 'Small molecules', 'uri': 'http://edamontology.org/topic_0154'}, {'term': 'DNA polymorphism', 'uri': 'http://edamontology.org/topic_2885'}, {'term': 'Proteomics', 'uri': 'http://edamontology.org/topic_0121'}]",[],1,[],False,False,[],"['Linux', 'Windows', 'Mac']",[],[],[],"[[['General'], 'https://en.wikipedia.org/wiki/ProRepeat']]",,False,False,['Jack A. M. Leunissen'],[]
modpropep,Server for structural modeling of protein kinases and MHC proteins in complex with their substrate peptides.,[],['Web application'],"[{'term': 'Small molecules', 'uri': 'http://edamontology.org/topic_0154'}, {'term': 'Proteins', 'uri': 'http://edamontology.org/topic_0078'}, {'term': 'Protein structure analysis', 'uri': 'http://edamontology.org/topic_2814'}, {'term': 'Proteomics', 'uri': 'http://edamontology.org/topic_0121'}, {'term': 'Sequence composition, complexity and repeats', 'uri': 'http://edamontology.org/topic_0157'}]",[],1,[],False,False,[],[],[],[],[],[],,False,False,[],[]
hslpred,Allows predicting the subcellular localization of human proteins. This is based on various type of residue composition of proteins using SVM technique.,[],['Web application'],"[{'term': 'Proteomics', 'uri': 'http://edamontology.org/topic_0121'}, {'term': 'Sequence composition, complexity and repeats', 'uri': 'http://edamontology.org/topic_0157'}, {'term': 'Sequence analysis', 'uri': 'http://edamontology.org/topic_0080'}, {'term': 'Cell biology', 'uri': 'http://edamontology.org/topic_2229'}]","[{'url': 'http://www.mybiosoftware.com/hslpred-svm-based-method-teh-subcellular-localization-human-proteins.html', 'note': None, 'type': ['Software catalogue']}]",1,[],False,False,[],"['Linux', 'Windows', 'Mac']",[],[],[],"[[['General'], 'http://crdd.osdd.net/raghava/hslpred/algo.html'], [['User manual'], 'http://crdd.osdd.net/raghava/hslpred/help.html']]",,False,False,['Dr. Raghava'],[]
hslpred,Allows predicting the subcellular localization of human proteins. This is based on various type of residue composition of proteins using SVM technique.,[],['Web application'],"[{'term': 'Proteomics', 'uri': 'http://edamontology.org/topic_0121'}, {'term': 'Sequence composition, complexity and repeats', 'uri': 'http://edamontology.org/topic_0157'}, {'term': 'Sequence analysis', 'uri': 'http://edamontology.org/topic_0080'}, {'term': 'Cell biology', 'uri': 'http://edamontology.org/topic_2229'}]","[{'url': 'http://www.mybiosoftware.com/hslpred-svm-based-method-teh-subcellular-localization-human-proteins.html', 'note': None, 'type': ['Software catalogue']}]",1,[],True,False,[],"['Linux', 'Windows', 'Mac']",[],[],[],"[[['General'], 'http://crdd.osdd.net/raghava/hslpred/algo.html'], [['User manual'], 'http://crdd.osdd.net/raghava/hslpred/help.html']]",,False,False,['Dr. Raghava'],[]
fasta,"The FASTA programs find regions of local or global similarity between protein or DNA sequences, either by searching protein or DNA databases, or by identifying local duplications within a sequence. Like BLAST, FASTA can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.",[],['Web application'],"[{'term': 'Sequence composition, complexity and repeats', 'uri': 'http://edamontology.org/topic_0157'}, {'term': 'Gene transcripts', 'uri': 'http://edamontology.org/topic_3512'}, {'term': 'Sequence analysis', 'uri': 'http://edamontology.org/topic_0080'}, {'term': 'Sequencing', 'uri': 'http://edamontology.org/topic_3168'}]","[{'url': 'https://fasta.bioch.virginia.edu/fasta_www2/fasta_mail.shtml', 'note': None, 'type': ['Mailing list']}]",3,"[['Downloads page', 'https://fasta.bioch.virginia.edu/fasta_www2/fasta_down.shtml']]",False,False,[],"['Linux', 'Windows', 'Mac']","[{'data': {'term': 'sequence', 'uri': 'http://edamontology.org/data_2044'}}]","[{'data': {'term': 'sequence', 'uri': 'http://edamontology.org/data_2044'}}]",[],"[[['General'], 'https://fasta.bioch.virginia.edu/fasta_www2/fasta_intro.shtml'], [['Release notes'], 'http://faculty.virginia.edu/wrpearson/fasta/changes_v36.html']]",,False,False,"['Support', 'Bill Pearson']",[]
snpmasker,Comprehensive web interface for masking SNPs and all low-complexity regions or repeats found in large eukaryotic genomes.,['1'],['Web application'],"[{'term': 'Sequence composition, complexity and repeats', 'uri': 'http://edamontology.org/topic_0157'}, {'term': 'Sequence analysis', 'uri': 'http://edamontology.org/topic_0080'}, {'term': 'DNA polymorphism', 'uri': 'http://edamontology.org/topic_2885'}]",[],1,[],False,False,[],"['Linux', 'Windows', 'Mac']","[{'data': {'term': 'sequence coordinates', 'uri': 'http://edamontology.org/data_2012'}}]","[{'data': {'term': 'sequence coordinates', 'uri': 'http://edamontology.org/data_2012'}}]",[],"[[['General'], 'http://bioinfo.ut.ee/snpmasker/']]",,False,False,"['ELIXIR-EE', 'Reidar Andreson']",[]
crisprs database,Gateway to publicly accessible CRISPRs database.,[],['Database portal'],"[{'term': 'Sequence composition, complexity and repeats', 'uri': 'http://edamontology.org/topic_0157'}, {'term': 'Transcription factors and regulatory sites', 'uri': 'http://edamontology.org/topic_0749'}, {'term': 'DNA polymorphism', 'uri': 'http://edamontology.org/topic_2885'}]",[],1,[],False,False,[],[],[],[],[],[],,False,False,['Christine Pourcel'],[]
interpro,"Protein families, domains, regions, repeats and sites in which identifiable features found in known proteins can be applied to new protein sequences.",[],['Database portal'],"[{'term': 'Gene and protein families', 'uri': 'http://edamontology.org/topic_0623'}, {'term': 'Proteins', 'uri': 'http://edamontology.org/topic_0078'}, {'term': 'Sequence composition, complexity and repeats', 'uri': 'http://edamontology.org/topic_0157'}]",[],1,[],False,False,[],"['Linux', 'Windows', 'Mac']","[{'data': {'term': 'interpro accession', 'uri': 'http://edamontology.org/data_1133'}}]","[{'data': {'term': 'interpro accession', 'uri': 'http://edamontology.org/data_1133'}}]",[],"[[['General'], 'http://www.ebi.ac.uk/interpro/training.html']]",,False,False,['EMBL-EBI Databases'],[]
pfam,Database which contains information about protein domains and families. For each entry a protein sequence alignment and a Hidden Markov Model is stored.,[],"['Web API', 'Web application', 'Database portal']","[{'term': 'Proteins', 'uri': 'http://edamontology.org/topic_0078'}, {'term': 'Gene and protein families', 'uri': 'http://edamontology.org/topic_0623'}, {'term': 'Protein folds and structural domains', 'uri': 'http://edamontology.org/topic_0736'}, {'term': 'Sequence sites, features and motifs', 'uri': 'http://edamontology.org/topic_0160'}, {'term': 'Sequence composition, complexity and repeats', 'uri': 'http://edamontology.org/topic_0157'}, {'term': 'Sequence analysis', 'uri': 'http://edamontology.org/topic_0080'}]","[{'url': 'http://pfam.sbc.su.se/', 'note': None, 'type': ['Mirror']}, {'url': 'http://pfam.jouy.inra.fr/', 'note': None, 'type': ['Mirror']}, {'url': 'http://pfam.sanger.ac.uk/', 'note': None, 'type': ['Mirror']}, {'url': 'http://pfam.ccbb.re.kr/index.shtml', 'note': None, 'type': ['Mirror']}, {'url': 'http://pfam.janelia.org/', 'note': None, 'type': ['Mirror']}]",2,[],False,False,[],"['Linux', 'Windows', 'Mac']","[{'data': {'term': 'pfam accession number', 'uri': 'http://edamontology.org/data_1138'}}]","[{'data': {'term': 'pfam accession number', 'uri': 'http://edamontology.org/data_1138'}}]",[],"[[['General'], 'http://www.ebi.ac.uk/about/terms-of-use']]",CC0-1.0,False,False,"['Identifiers.org', 'EMBL-EBI Databases', 'Sean Eddy', 'Pfam group', 'Sanger Institute', 'HHMI', 'Pfam central helpdesk', 'How to contact Pfam']",[]
repeatsdb,Database of annotated tandem repeat protein structures.,['2.0'],"['Web API', 'Web application', 'Database portal']","[{'term': 'Protein structure analysis', 'uri': 'http://edamontology.org/topic_2814'}, {'term': 'Sequence composition, complexity and repeats', 'uri': 'http://edamontology.org/topic_0157'}]",[],1,[],False,False,[],"['Linux', 'Windows', 'Mac']","[{'data': {'term': 'pdb id', 'uri': 'http://edamontology.org/data_1127'}}]","[{'data': {'term': 'pdb id', 'uri': 'http://edamontology.org/data_1127'}}]",[],"[[['General'], 'http://repeatsdb.bio.unipd.it/help']]",,False,False,"['University of Padua, Department of Biomedical Sciences, BioComputing UP lab', 'ELIXIR-ITA-PADOVA', 'Silvio C.E. Tosatto']",[]
reputer,The repetitive structure of genomic DNA holds many secrets to be discovered. A systematic study of repetitive DNA on a genomic or inter-genomic scale requires extensive algorithmic support. The REPuter program was designed to serve as a fundamental tool in such studies. Efficient and complete detection of various types of repeats is provided together with an evaluation of significance and interactive visualization.,['1'],"['Web API', 'Web application', 'Command-line tool']","[{'term': 'Sequence composition, complexity and repeats', 'uri': 'http://edamontology.org/topic_0157'}, {'term': 'DNA', 'uri': 'http://edamontology.org/topic_0654'}, {'term': 'Genomics', 'uri': 'http://edamontology.org/topic_0622'}]","[{'url': 'http://bibiserv.cebitec.uni-bielefeld.de/reputer?id=reputer_view_download', 'note': None, 'type': ['Repository']}, {'url': 'http://www.mybiosoftware.com/reputer-compute-visualize-repeat-structures.html', 'note': None, 'type': ['Software catalogue']}]",1,"[['Source code', 'http://bibiserv.cebitec.uni-bielefeld.de/reputer?id=reputer_view_download'], ['Binaries', 'http://bibiserv.cebitec.uni-bielefeld.de/reputer?id=reputer_view_download']]",False,False,['http://bibiserv.cebitec.uni-bielefeld.de/reputer?id=reputer_view_download'],"['Linux', 'Mac']","[{'data': {'term': 'nucleic acid sequence (raw)', 'uri': 'http://edamontology.org/data_2975'}, 'format': {'term': 'unambiguous pure dna', 'uri': 'http://edamontology.org/format_1214'}}]","[{'data': {'term': 'nucleic acid sequence (raw)', 'uri': 'http://edamontology.org/data_2975'}, 'format': {'term': 'unambiguous pure dna', 'uri': 'http://edamontology.org/format_1214'}}]",[],"[[['User manual'], 'http://bibiserv.cebitec.uni-bielefeld.de/reputer?id=reputer_manual_manual']]",,False,False,['BiBiServ'],['http://bibiserv.cebitec.uni-bielefeld.de/reputer?id=reputer_view_download']
reputer,The repetitive structure of genomic DNA holds many secrets to be discovered. A systematic study of repetitive DNA on a genomic or inter-genomic scale requires extensive algorithmic support. The REPuter program was designed to serve as a fundamental tool in such studies. Efficient and complete detection of various types of repeats is provided together with an evaluation of significance and interactive visualization.,['1'],"['Web API', 'Web application', 'Command-line tool']","[{'term': 'Sequence composition, complexity and repeats', 'uri': 'http://edamontology.org/topic_0157'}, {'term': 'DNA', 'uri': 'http://edamontology.org/topic_0654'}, {'term': 'Genomics', 'uri': 'http://edamontology.org/topic_0622'}]","[{'url': 'http://bibiserv.cebitec.uni-bielefeld.de/reputer?id=reputer_view_download', 'note': None, 'type': ['Repository']}, {'url': 'http://www.mybiosoftware.com/reputer-compute-visualize-repeat-structures.html', 'note': None, 'type': ['Software catalogue']}]",1,"[['Source code', 'http://bibiserv.cebitec.uni-bielefeld.de/reputer?id=reputer_view_download'], ['Binaries', 'http://bibiserv.cebitec.uni-bielefeld.de/reputer?id=reputer_view_download']]",False,False,['http://bibiserv.cebitec.uni-bielefeld.de/reputer?id=reputer_view_download'],"['Linux', 'Mac']","[{'data': {'term': 'nucleic acid sequence (raw)', 'uri': 'http://edamontology.org/data_2975'}, 'format': {'term': 'unambiguous pure dna', 'uri': 'http://edamontology.org/format_1214'}}]","[{'data': {'term': 'nucleic acid sequence (raw)', 'uri': 'http://edamontology.org/data_2975'}, 'format': {'term': 'unambiguous pure dna', 'uri': 'http://edamontology.org/format_1214'}}]",[],"[[['User manual'], 'http://bibiserv.cebitec.uni-bielefeld.de/reputer?id=reputer_manual_manual']]",,False,False,['BiBiServ'],['http://bibiserv.cebitec.uni-bielefeld.de/reputer?id=reputer_view_download']
reputer,The repetitive structure of genomic DNA holds many secrets to be discovered. A systematic study of repetitive DNA on a genomic or inter-genomic scale requires extensive algorithmic support. The REPuter program was designed to serve as a fundamental tool in such studies. Efficient and complete detection of various types of repeats is provided together with an evaluation of significance and interactive visualization.,['1'],"['Web API', 'Web application', 'Command-line tool']","[{'term': 'Sequence composition, complexity and repeats', 'uri': 'http://edamontology.org/topic_0157'}, {'term': 'DNA', 'uri': 'http://edamontology.org/topic_0654'}, {'term': 'Genomics', 'uri': 'http://edamontology.org/topic_0622'}]","[{'url': 'http://bibiserv.cebitec.uni-bielefeld.de/reputer?id=reputer_view_download', 'note': None, 'type': ['Repository']}, {'url': 'http://www.mybiosoftware.com/reputer-compute-visualize-repeat-structures.html', 'note': None, 'type': ['Software catalogue']}]",1,"[['Source code', 'http://bibiserv.cebitec.uni-bielefeld.de/reputer?id=reputer_view_download'], ['Binaries', 'http://bibiserv.cebitec.uni-bielefeld.de/reputer?id=reputer_view_download']]",True,False,['http://bibiserv.cebitec.uni-bielefeld.de/reputer?id=reputer_view_download'],"['Linux', 'Mac']","[{'data': {'term': 'nucleic acid sequence (raw)', 'uri': 'http://edamontology.org/data_2975'}, 'format': {'term': 'unambiguous pure dna', 'uri': 'http://edamontology.org/format_1214'}}]","[{'data': {'term': 'nucleic acid sequence (raw)', 'uri': 'http://edamontology.org/data_2975'}, 'format': {'term': 'unambiguous pure dna', 'uri': 'http://edamontology.org/format_1214'}}]",[],"[[['User manual'], 'http://bibiserv.cebitec.uni-bielefeld.de/reputer?id=reputer_manual_manual']]",,False,False,['BiBiServ'],['http://bibiserv.cebitec.uni-bielefeld.de/reputer?id=reputer_view_download']
reputer,The repetitive structure of genomic DNA holds many secrets to be discovered. A systematic study of repetitive DNA on a genomic or inter-genomic scale requires extensive algorithmic support. The REPuter program was designed to serve as a fundamental tool in such studies. Efficient and complete detection of various types of repeats is provided together with an evaluation of significance and interactive visualization.,['1'],"['Web API', 'Web application', 'Command-line tool']","[{'term': 'Sequence composition, complexity and repeats', 'uri': 'http://edamontology.org/topic_0157'}, {'term': 'DNA', 'uri': 'http://edamontology.org/topic_0654'}, {'term': 'Genomics', 'uri': 'http://edamontology.org/topic_0622'}]","[{'url': 'http://bibiserv.cebitec.uni-bielefeld.de/reputer?id=reputer_view_download', 'note': None, 'type': ['Repository']}, {'url': 'http://www.mybiosoftware.com/reputer-compute-visualize-repeat-structures.html', 'note': None, 'type': ['Software catalogue']}]",1,"[['Source code', 'http://bibiserv.cebitec.uni-bielefeld.de/reputer?id=reputer_view_download'], ['Binaries', 'http://bibiserv.cebitec.uni-bielefeld.de/reputer?id=reputer_view_download']]",True,False,['http://bibiserv.cebitec.uni-bielefeld.de/reputer?id=reputer_view_download'],"['Linux', 'Mac']","[{'data': {'term': 'nucleic acid sequence (raw)', 'uri': 'http://edamontology.org/data_2975'}, 'format': {'term': 'unambiguous pure dna', 'uri': 'http://edamontology.org/format_1214'}}]","[{'data': {'term': 'nucleic acid sequence (raw)', 'uri': 'http://edamontology.org/data_2975'}, 'format': {'term': 'unambiguous pure dna', 'uri': 'http://edamontology.org/format_1214'}}]",[],"[[['User manual'], 'http://bibiserv.cebitec.uni-bielefeld.de/reputer?id=reputer_manual_manual']]",,False,False,['BiBiServ'],['http://bibiserv.cebitec.uni-bielefeld.de/reputer?id=reputer_view_download']
radar,Identify gapped approximate repeats and complex repeat architectures involving many different types of repeats.,['1'],['Web application'],"[{'term': 'Sequence composition, complexity and repeats', 'uri': 'http://edamontology.org/topic_0157'}]","[{'url': 'http://www.ebi.ac.uk/support/', 'note': None, 'type': ['Helpdesk']}]",1,[],False,False,[],"['Linux', 'Windows', 'Mac']","[{'data': {'term': 'protein sequence', 'uri': 'http://edamontology.org/data_2976'}}]","[{'data': {'term': 'protein sequence', 'uri': 'http://edamontology.org/data_2976'}}]",[],"[[['Terms of use'], 'http://www.ebi.ac.uk/about/terms-of-use'], [['General'], 'http://www.ebi.ac.uk/Tools/pfa/radar/']]",,False,False,"['Andreas Heger', 'Web Production', 'EMBL-EBI']",[]
trdistiller,A rapid filter that is based on the comparison of composition and order of short strings in the adjacent sequence motifs.,[],['Command-line tool'],"[{'term': 'DNA polymorphism', 'uri': 'http://edamontology.org/topic_2885'}, {'term': 'Sequence composition, complexity and repeats', 'uri': 'http://edamontology.org/topic_0157'}, {'term': 'Sequence analysis', 'uri': 'http://edamontology.org/topic_0080'}]","[{'url': 'http://www.mybiosoftware.com/trdistiller-tandem-repeats-detection.html', 'note': None, 'type': ['Software catalogue']}]",1,[],False,False,[],"['Linux', 'Mac']",[],[],[],"[[['General'], 'http://bioinfo.montp.cnrs.fr/?r=TRDistiller']]",,False,False,[],[]
gcat,"Genetic Code Analysis Toolkit (GCAT) which provides workflows and algorithms for the analysis of the structure of nucleotide sequences. In particular, sets or sequences of codons can be transformed and tested for circularity, comma-freeness, dichotomic partitions and others. GCAT comes with a fertile editor custom-built to work with the genetic code and a batch mode for multi-sequence processing.",['2.0'],['Desktop application'],"[{'term': 'Sequence composition, complexity and repeats', 'uri': 'http://edamontology.org/topic_0157'}, {'term': 'Sequence assembly', 'uri': 'http://edamontology.org/topic_0196'}]","[{'url': 'https://github.com/informatik-mannheim/genetic-code-analysis-toolkit/issues', 'note': None, 'type': ['Issue tracker']}]",1,[],False,False,[],"['Linux', 'Windows', 'Mac']",[],[],[],"[[['General'], 'https://github.com/informatik-mannheim/genetic-code-analysis-toolkit/blob/master/README.md']]",Apache-2.0,False,False,[],[]
......@@ -97,9 +97,9 @@ vivaxgen,Open access platform for comparative analysis of short tandem repeat ge
lrrsearch,An asynchronous server-based application for the prediction of leucine-rich repeat motifs and an integrative database of NOD-like receptors.,[],"['Web application', 'Database portal']","[{'term': 'Protein sites, features and motifs', 'uri': 'http://edamontology.org/topic_3510'}, {'term': 'Sequence composition, complexity and repeats', 'uri': 'http://edamontology.org/topic_0157'}, {'term': 'Proteins', 'uri': 'http://edamontology.org/topic_0078'}]",[],1,[],False,False,[],"['Linux', 'Windows', 'Mac']",[],[],[],"[[['General'], 'http://www.lrrsearch.com/index.php?page=about']]",,False,False,['Support'],[]
detectir,A tool for detecting perfect and imperfect inverted repeats in genomes.,[],['Script'],"[{'term': 'DNA structural variation', 'uri': 'http://edamontology.org/topic_3175'}, {'term': 'Sequence composition, complexity and repeats', 'uri': 'http://edamontology.org/topic_0157'}]",[],1,"[['Source code', 'https://sourceforge.net/projects/detectir/']]",False,False,['https://sourceforge.net/projects/detectir/'],"['Linux', 'Windows']",[],[],[],"[[['General'], 'https://sourceforge.net/p/detectir/wiki/User%20Manual/']]",CC-BY-NC-SA-3.0,False,False,['Dr. Chun Liang'],[]
esap plus,A web-based server for EST-SSR marker development.,[],['Web application'],"[{'term': 'Sequence composition, complexity and repeats', 'uri': 'http://edamontology.org/topic_0157'}, {'term': 'Sequence sites, features and motifs', 'uri': 'http://edamontology.org/topic_0160'}, {'term': 'Molecular genetics', 'uri': 'http://edamontology.org/topic_3321'}]",[],1,[],False,False,[],"['Linux', 'Windows', 'Mac']",[],[],[],[],GPL-3.0,False,False,['Contact form'],[]
spotyping,Fast and accurate in silico Mycobacterium spoligotyping from sequence reads.,['2.0'],['Command-line tool'],"[{'term': 'Microbiology', 'uri': 'http://edamontology.org/topic_3301'}, {'term': 'Sequencing', 'uri': 'http://edamontology.org/topic_3168'}, {'term': 'Sequence composition, complexity and repeats', 'uri': 'http://edamontology.org/topic_0157'}, {'term': 'Genetic variation', 'uri': 'http://edamontology.org/topic_0199'}]",[],1,[],False,False,[],"['Linux', 'Mac']",[],[],[],"[[['User manual'], 'https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine']]",,False,False,['Rick Twee-Hee Ong'],[]
spotyping,Fast and accurate in silico Mycobacterium spoligotyping from sequence reads.,['2.0'],['Command-line tool'],"[{'term': 'Microbiology', 'uri': 'http://edamontology.org/topic_3301'}, {'term': 'Sequencing', 'uri': 'http://edamontology.org/topic_3168'}, {'term': 'Sequence composition, complexity and repeats', 'uri': 'http://edamontology.org/topic_0157'}, {'term': 'Genetic variation', 'uri': 'http://edamontology.org/topic_0199'}]",[],1,[],True,False,[],"['Linux', 'Mac']",[],[],[],"[[['User manual'], 'https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine']]",,False,False,['Rick Twee-Hee Ong'],[]
sewer,"Sequence analysis tools on the web; includes nucleic acid, protein, PCR and alignment tools.",[],['Web application'],"[{'term': 'Nucleic acids', 'uri': 'http://edamontology.org/topic_0077'}, {'term': 'Sequence analysis', 'uri': 'http://edamontology.org/topic_0080'}, {'term': 'Sequence composition, complexity and repeats', 'uri': 'http://edamontology.org/topic_0157'}, {'term': 'Nucleic acid structure analysis', 'uri': 'http://edamontology.org/topic_0097'}, {'term': 'Nucleic acid sites, features and motifs', 'uri': 'http://edamontology.org/topic_3511'}]",[],1,[],False,False,[],"['Linux', 'Windows', 'Mac']",[],[],[],[],,False,False,['Malay K Basu'],[]
gream,"A Web Server to Short-List Potentially Important Genomic Repeat Elements Based on Over-/Under-Representation in Specific Chromosomal Locations, Such as the Gene Neighborhoods, within or across 17 Mammalian Species",[],['Web application'],"[{'term': 'Genomics', 'uri': 'http://edamontology.org/topic_0622'}, {'term': 'Sequence composition, complexity and repeats', 'uri': 'http://edamontology.org/topic_0157'}, {'term': 'Sequence analysis', 'uri': 'http://edamontology.org/topic_0080'}]",[],1,[],False,False,[],"['Linux', 'Windows', 'Mac']",[],[],[],"[[['User manual'], 'http://resource.ibab.ac.in/cgi-bin/GREAM/userguide.pl']]",,False,False,['Kshitish K. Acharya'],[]
gream,"A Web Server to Short-List Potentially Important Genomic Repeat Elements Based on Over-/Under-Representation in Specific Chromosomal Locations, Such as the Gene Neighborhoods, within or across 17 Mammalian Species",[],['Web application'],"[{'term': 'Genomics', 'uri': 'http://edamontology.org/topic_0622'}, {'term': 'Sequence composition, complexity and repeats', 'uri': 'http://edamontology.org/topic_0157'}, {'term': 'Sequence analysis', 'uri': 'http://edamontology.org/topic_0080'}]",[],1,[],True,False,[],"['Linux', 'Windows', 'Mac']",[],[],[],"[[['User manual'], 'http://resource.ibab.ac.in/cgi-bin/GREAM/userguide.pl']]",,False,False,['Kshitish K. Acharya'],[]
mreps,mreps is a tool for identifing tandemn repeats in DNA sequences.,[],['Web application'],"[{'term': 'DNA polymorphism', 'uri': 'http://edamontology.org/topic_2885'}, {'term': 'Sequence composition, complexity and repeats', 'uri': 'http://edamontology.org/topic_0157'}, {'term': 'DNA', 'uri': 'http://edamontology.org/topic_0654'}, {'term': 'Sequencing', 'uri': 'http://edamontology.org/topic_3168'}, {'term': 'Genetic variation', 'uri': 'http://edamontology.org/topic_0199'}]",[],1,[],False,False,[],"['Linux', 'Windows', 'Mac']",[],[],[],"[[['General'], 'http://mreps.univ-mlv.fr/tutorial.html']]",,False,False,['Gregory Kucherov'],[]
comsin,"ComSin is a database of protein structures in bound (complex) and unbound (single) states. The developed server enables one to search for proteins in bound and unbound states with several options including sequence similarity between the corresponding proteins in bound and unbound states, and validation of interaction interfaces of protein complexes.",[],['Database portal'],"[{'term': 'Proteins', 'uri': 'http://edamontology.org/topic_0078'}, {'term': 'Protein structure analysis', 'uri': 'http://edamontology.org/topic_2814'}, {'term': 'Protein disordered structure', 'uri': 'http://edamontology.org/topic_3538'}, {'term': 'Protein folds and structural domains', 'uri': 'http://edamontology.org/topic_0736'}, {'term': 'Sequence composition, complexity and repeats', 'uri': 'http://edamontology.org/topic_0157'}]",[],1,[],False,False,[],"['Linux', 'Windows', 'Mac']",[],[],[],"[[['General'], 'http://antares.protres.ru/comsin/about.html']]",,False,False,['Michail Yu. Lobanov'],[]
semgen,An experimental software tool for automating the modular composition and decomposition of biosimulation models.,[],['Desktop application'],"[{'term': 'Systems biology', 'uri': 'http://edamontology.org/topic_2259'}, {'term': 'Simulation experiment', 'uri': 'http://edamontology.org/topic_3524'}, {'term': 'Sequence composition, complexity and repeats', 'uri': 'http://edamontology.org/topic_0157'}]","[{'url': 'http://www.mybiosoftware.com/semgen-1-3-semantics-biological-processes.html', 'note': None, 'type': ['Software catalogue']}]",1,[],False,False,[],"['Linux', 'Windows', 'Mac']",[],[],[],"[[['General'], 'http://sbp.bhi.washington.edu/projects/semgen/semgenhelp']]",,False,False,[],[]
......@@ -114,7 +114,7 @@ nucleic acid database (ndb),NDB (Nucleic Acid Database) is a repository of three
ndb tools,"The Nucleic Acid Database (NDB) Tools page includes RNAView and BPView, programs for the visualization and classification of RNA base pairs, motifs, and structures.",[],['Web application'],"[{'term': 'Nucleic acid structure analysis', 'uri': 'http://edamontology.org/topic_0097'}, {'term': 'Nucleic acids', 'uri': 'http://edamontology.org/topic_0077'}, {'term': 'Structure prediction', 'uri': 'http://edamontology.org/topic_0082'}, {'term': 'Sequence composition, complexity and repeats', 'uri': 'http://edamontology.org/topic_0157'}, {'term': 'Nucleic acid sites, features and motifs', 'uri': 'http://edamontology.org/topic_3511'}]",[],3,[],False,False,[],"['Linux', 'Windows', 'Mac']",[],[],[],"[[['General'], 'http://ndbserver.rutgers.edu/ndbmodule/about_ndb/about.html']]",,False,False,['NDB Admin'],[]
disulfind,DISULFIND is a server for predicting the disulfide bonding state of cysteines and their disulfide connectivity given a protein sequence.,[],['Web application'],"[{'term': 'Proteins', 'uri': 'http://edamontology.org/topic_0078'}, {'term': 'Protein sites, features and motifs', 'uri': 'http://edamontology.org/topic_3510'}, {'term': 'Sequence composition, complexity and repeats', 'uri': 'http://edamontology.org/topic_0157'}, {'term': 'Gene and protein families', 'uri': 'http://edamontology.org/topic_0623'}, {'term': 'Structure prediction', 'uri': 'http://edamontology.org/topic_0082'}]",[],4,[],False,False,[],"['Linux', 'Windows', 'Mac']",[],[],[],"[[['General'], 'http://disulfind.dsi.unifi.it/help.php']]",,False,False,['DISULFIND Support'],[]
pcfamily,"The PCFamily server identifies template-based homologous protein complexes or families, and infers functional modules for query proteins. Useful for binding model visualizations and annotating query proteins.",[],['Web application'],"[{'term': 'Molecular modelling', 'uri': 'http://edamontology.org/topic_2275'}, {'term': 'Gene and protein families', 'uri': 'http://edamontology.org/topic_0623'}, {'term': 'Proteins', 'uri': 'http://edamontology.org/topic_0078'}, {'term': 'Molecular interactions, pathways and networks', 'uri': 'http://edamontology.org/topic_0602'}, {'term': 'Sequence composition, complexity and repeats', 'uri': 'http://edamontology.org/topic_0157'}]",[],1,[],False,False,[],"['Linux', 'Windows', 'Mac']",[],[],[],"[[['General'], 'http://pcfamily.life.nctu.edu.tw/help.php']]",,False,False,['PCFamily Support'],[]
curves+,Curves+ is a web server for the analysis and visualization of the helical backbone and groove parameters of nucleic acid structures.,[],['Web application'],"[{'term': 'Nucleic acid structure analysis', 'uri': 'http://edamontology.org/topic_0097'}, {'term': 'Nucleic acids', 'uri': 'http://edamontology.org/topic_0077'}, {'term': 'Structure prediction', 'uri': 'http://edamontology.org/topic_0082'}, {'term': 'Sequence composition, complexity and repeats', 'uri': 'http://edamontology.org/topic_0157'}, {'term': 'Nucleic acid sites, features and motifs', 'uri': 'http://edamontology.org/topic_3511'}]",[],1,[],False,False,[],"['Linux', 'Windows', 'Mac']",[],[],[],"[[['User manual'], 'https://bisi.ibcp.fr/tools/curves_plus/canal-user-guide.html'], [['User manual'], 'https://bisi.ibcp.fr/tools/curves_plus/curves-user-guide.html'], [['User manual'], 'https://bisi.ibcp.fr/tools/curves_plus/canion-user-guide.html']]",,False,False,['R. Lavery'],[]
curves+,Curves+ is a web server for the analysis and visualization of the helical backbone and groove parameters of nucleic acid structures.,[],['Web application'],"[{'term': 'Nucleic acid structure analysis', 'uri': 'http://edamontology.org/topic_0097'}, {'term': 'Nucleic acids', 'uri': 'http://edamontology.org/topic_0077'}, {'term': 'Structure prediction', 'uri': 'http://edamontology.org/topic_0082'}, {'term': 'Sequence composition, complexity and repeats', 'uri': 'http://edamontology.org/topic_0157'}, {'term': 'Nucleic acid sites, features and motifs', 'uri': 'http://edamontology.org/topic_3511'}]",[],1,[],True,False,[],"['Linux', 'Windows', 'Mac']",[],[],[],"[[['User manual'], 'https://bisi.ibcp.fr/tools/curves_plus/canal-user-guide.html'], [['User manual'], 'https://bisi.ibcp.fr/tools/curves_plus/curves-user-guide.html'], [['User manual'], 'https://bisi.ibcp.fr/tools/curves_plus/canion-user-guide.html']]",,False,False,['R. Lavery'],[]
qgrs mapper,Quadruplex forming G-Rich Sequences (QGRS) Mapper searches nucleotide sequences for the presence of G-quartet motifs. QGRS Mapper allows you to view the distribution and composition of QGRS in the context of alternatively spliced isoforms of your gene.,[],['Web application'],"[{'term': 'RNA splicing', 'uri': 'http://edamontology.org/topic_3320'}, {'term': 'Sequence analysis', 'uri': 'http://edamontology.org/topic_0080'}, {'term': 'Sequence composition, complexity and repeats', 'uri': 'http://edamontology.org/topic_0157'}, {'term': 'Sequencing', 'uri': 'http://edamontology.org/topic_3168'}, {'term': 'Sequence sites, features and motifs', 'uri': 'http://edamontology.org/topic_0160'}]",[],1,[],False,False,[],"['Linux', 'Windows', 'Mac']",[],[],[],"[[['General'], 'http://bioinformatics.ramapo.edu/QGRS/help.php']]",,False,False,"['Paramjeet Bagga', ""Lawrence D'Antonio"", 'Oleg Kikin', 'Manuel Viotti']",[]
gpcrsclass,Tool for predicting amine-binding receptors based on a protein sequence provided by the user.,[],['Web application'],"[{'term': 'Proteins', 'uri': 'http://edamontology.org/topic_0078'}, {'term': 'Protein sites, features and motifs', 'uri': 'http://edamontology.org/topic_3510'}, {'term': 'Sequence composition, complexity and repeats', 'uri': 'http://edamontology.org/topic_0157'}, {'term': 'Gene and protein families', 'uri': 'http://edamontology.org/topic_0623'}, {'term': 'Structure prediction', 'uri': 'http://edamontology.org/topic_0082'}]",[],1,[],False,False,[],"['Linux', 'Windows', 'Mac']",[],[],[],"[[['General'], 'http://crdd.osdd.net/raghava/gpcrsclass/help.html']]",,False,False,['G.P.S. Raghava'],[]
corgen,Measures long-range correlations in DNA sequences and can generate random sequences with the same (or user-specified) correlation and composition parameters.,[],['Web application'],"[{'term': 'DNA', 'uri': 'http://edamontology.org/topic_0654'}, {'term': 'Sequence composition, complexity and repeats', 'uri': 'http://edamontology.org/topic_0157'}, {'term': 'Sequence analysis', 'uri': 'http://edamontology.org/topic_0080'}, {'term': 'Sequencing', 'uri': 'http://edamontology.org/topic_3168'}]",[],1,[],False,False,[],"['Linux', 'Windows', 'Mac']",[],[],[],"[[['General'], 'http://corgen.molgen.mpg.de/']]",,False,False,['Philipp W. Messer'],[]
......@@ -124,11 +124,11 @@ pubcrawler,It goes to the library. You go to the pub; receive email alerts for c
acg,The Ancestral Recombination Graph tool is a graphical desktop application that allows genetics researchers to infer properties of a population based on genetic sequences sampled from it.,[],['Desktop application'],"[{'term': 'Population genetics', 'uri': 'http://edamontology.org/topic_3056'}, {'term': 'Sequence composition, complexity and repeats', 'uri': 'http://edamontology.org/topic_0157'}]","[{'url': 'http://www.mybiosoftware.com/acg-inference-of-population-history-from-genetic-data.html', 'note': None, 'type': ['Software catalogue']}]",1,[],False,False,[],"['Linux', 'Windows', 'Mac']",[],[],[],"[[['General'], 'http://arup.utah.edu/ACG/tutorial.html']]",,False,False,"[""Brendan O'Fallon""]",[]
doutfinder,Tool for facilitating protein domain detection among remotely related protein sequences.,[],['Web application'],"[{'term': 'Protein folds and structural domains', 'uri': 'http://edamontology.org/topic_0736'}, {'term': 'Proteins', 'uri': 'http://edamontology.org/topic_0078'}, {'term': 'Protein sites, features and motifs', 'uri': 'http://edamontology.org/topic_3510'}, {'term': 'Protein structure analysis', 'uri': 'http://edamontology.org/topic_2814'}, {'term': 'Sequence composition, complexity and repeats', 'uri': 'http://edamontology.org/topic_0157'}]",[],1,[],False,False,[],"['Linux', 'Windows', 'Mac']",[],[],[],"[[['General'], 'http://mendel.imp.ac.at/dout/']]",,False,False,['Support'],[]
proteus,An archive of functional signatures in protein termini.,[],['Web application'],"[{'term': 'Proteins', 'uri': 'http://edamontology.org/topic_0078'}, {'term': 'Protein targeting and localisation', 'uri': 'http://edamontology.org/topic_0140'}, {'term': 'Function analysis', 'uri': 'http://edamontology.org/topic_1775'}, {'term': 'Protein binding sites', 'uri': 'http://edamontology.org/topic_3534'}, {'term': 'Sequence composition, complexity and repeats', 'uri': 'http://edamontology.org/topic_0157'}]",[],1,[],False,False,[],"['Linux', 'Windows', 'Mac']",[],[],[],"[[['General'], 'http://www.proteus.cs.huji.ac.il/glossary.php']]",,False,False,['Michal Linial'],[]
protinfo ppc,Protinfo Prediction of Protein Complex (PPC) is a web server that predicts atomic level structures of interacting proteins from their amino acid sequences.,[],['Web application'],"[{'term': 'Structure prediction', 'uri': 'http://edamontology.org/topic_0082'}, {'term': 'Protein interactions', 'uri': 'http://edamontology.org/topic_0128'}, {'term': 'Molecular modelling', 'uri': 'http://edamontology.org/topic_2275'}, {'term': 'Molecular interactions, pathways and networks', 'uri': 'http://edamontology.org/topic_0602'}, {'term': 'Sequence composition, complexity and repeats', 'uri': 'http://edamontology.org/topic_0157'}]",[],1,[],False,False,[],"['Linux', 'Windows', 'Mac']",[],[],[],"[[['User manual'], 'http://protinfo.compbio.buffalo.edu/ppc/tutorial.html']]",,False,False,['Protoinfo Support'],[]
protinfo ppc,Protinfo Prediction of Protein Complex (PPC) is a web server that predicts atomic level structures of interacting proteins from their amino acid sequences.,[],['Web application'],"[{'term': 'Structure prediction', 'uri': 'http://edamontology.org/topic_0082'}, {'term': 'Protein interactions', 'uri': 'http://edamontology.org/topic_0128'}, {'term': 'Molecular modelling', 'uri': 'http://edamontology.org/topic_2275'}, {'term': 'Molecular interactions, pathways and networks', 'uri': 'http://edamontology.org/topic_0602'}, {'term': 'Sequence composition, complexity and repeats', 'uri': 'http://edamontology.org/topic_0157'}]",[],1,[],True,False,[],"['Linux', 'Windows', 'Mac']",[],[],[],"[[['User manual'], 'http://protinfo.compbio.buffalo.edu/ppc/tutorial.html']]",,False,False,['Protoinfo Support'],[]
repeatoire,A software on a hybrid data set of real genomic DNA with simulated interspersed repeats.,[],['Command-line tool'],"[{'term': 'DNA', 'uri': 'http://edamontology.org/topic_0654'}, {'term': 'Sequence composition, complexity and repeats', 'uri': 'http://edamontology.org/topic_0157'}, {'term': 'Nucleic acid structure analysis', 'uri': 'http://edamontology.org/topic_0097'}, {'term': 'Genomics', 'uri': 'http://edamontology.org/topic_0622'}]","[{'url': 'http://www.mybiosoftware.com/repeatoire-ab-inito-prediction-repeat-families.html', 'note': None, 'type': ['Software catalogue']}]",1,[],False,False,[],"['Linux', 'Mac']",[],[],[],"[[['General'], 'http://wwwabi.snv.jussieu.fr/public/Repeatoire/']]",,False,False,[],[]
eslpred,"Tool for predicting subcellular localization of proteins using support vector machines. The predictions are based on dipeptide and amino acid composition, and physico-chemical properties.",[],['Web application'],"[{'term': 'Machine learning', 'uri': 'http://edamontology.org/topic_3474'}, {'term': 'Small molecules', 'uri': 'http://edamontology.org/topic_0154'}, {'term': 'Proteins', 'uri': 'http://edamontology.org/topic_0078'}, {'term': 'Protein properties', 'uri': 'http://edamontology.org/topic_0123'}, {'term': 'Sequence composition, complexity and repeats', 'uri': 'http://edamontology.org/topic_0157'}]",[],1,[],False,False,[],"['Linux', 'Windows', 'Mac']",[],[],[],"[[['General'], 'http://crdd.osdd.net/raghava/eslpred/help.html']]",,False,False,['G.P.S. Raghava'],[]
strap,"The Structural Alignment Program for Proteins (STRAP) is a java-based program that can be run over the web using a Java Web Start enabled browser or downloaded and run as a stand-alone application. Alignments can be done using one of several methods, including ClustalW, JAligner and T_coffee. STRAP is also able to incorporate structure information and interfaces with programs such as Pymol and Rasmol. There is also a tutorial included.",[],['Web application'],"[{'term': 'Proteins', 'uri': 'http://edamontology.org/topic_0078'}, {'term': 'Sequence composition, complexity and repeats', 'uri': 'http://edamontology.org/topic_0157'}, {'term': 'Gene and protein families', 'uri': 'http://edamontology.org/topic_0623'}, {'term': 'Nucleic acid structure analysis', 'uri': 'http://edamontology.org/topic_0097'}]",[],2,[],False,False,[],"['Linux', 'Windows', 'Mac']",[],[],[],"[[['General'], 'http://www.bioinformatics.org/strap/security.html']]",,False,False,['Christoph Gille'],[]
genebreak,Recurrent breakpoint gene detection on copy number aberration profiles.,['1.4'],"['Command-line tool', 'Library']","[{'term': 'DNA structural variation', 'uri': 'http://edamontology.org/topic_3175'}, {'term': 'Sequence composition, complexity and repeats', 'uri': 'http://edamontology.org/topic_0157'}]","[{'url': 'https://github.com/stefvanlieshout/GeneBreak', 'note': None, 'type': ['Mirror']}]",1,"[['Source code', 'http://bioconductor/packages/release/bioc/src/contrib/GeneBreak_1.4.0.tar.gz']]",False,False,['http://bioconductor/packages/release/bioc/src/contrib/GeneBreak_1.4.0.tar.gz'],"['Linux', 'Windows', 'Mac']","[{'data': {'term': 'gene report', 'uri': 'http://edamontology.org/data_0916'}, 'format': {'term': 'textual format', 'uri': 'http://edamontology.org/format_2330'}}]","[{'data': {'term': 'gene report', 'uri': 'http://edamontology.org/data_0916'}, 'format': {'term': 'textual format', 'uri': 'http://edamontology.org/format_2330'}}]",[],"[[['User manual'], 'http://bioconductor.org/packages/release/bioc/html/GeneBreak.html']]",GPL-2.0,False,False,['Evert van den Broek'],[]
genebreak,Recurrent breakpoint gene detection on copy number aberration profiles.,['1.4'],"['Command-line tool', 'Library']","[{'term': 'DNA structural variation', 'uri': 'http://edamontology.org/topic_3175'}, {'term': 'Sequence composition, complexity and repeats', 'uri': 'http://edamontology.org/topic_0157'}]","[{'url': 'https://github.com/stefvanlieshout/GeneBreak', 'note': None, 'type': ['Mirror']}]",1,"[['Source code', 'http://bioconductor/packages/release/bioc/src/contrib/GeneBreak_1.4.0.tar.gz']]",True,False,['http://bioconductor/packages/release/bioc/src/contrib/GeneBreak_1.4.0.tar.gz'],"['Linux', 'Windows', 'Mac']","[{'data': {'term': 'gene report', 'uri': 'http://edamontology.org/data_0916'}, 'format': {'term': 'textual format', 'uri': 'http://edamontology.org/format_2330'}}]","[{'data': {'term': 'gene report', 'uri': 'http://edamontology.org/data_0916'}, 'format': {'term': 'textual format', 'uri': 'http://edamontology.org/format_2330'}}]",[],"[[['User manual'], 'http://bioconductor.org/packages/release/bioc/html/GeneBreak.html']]",GPL-2.0,False,False,['Evert van den Broek'],[]
subseqer,Tool to find sequence motifs in low complexity protein sequences. It uses the application of a unique graph based approach.,[],['Web application'],"[{'term': 'Sequence composition, complexity and repeats', 'uri': 'http://edamontology.org/topic_0157'}, {'term': 'Sequence sites, features and motifs', 'uri': 'http://edamontology.org/topic_0160'}, {'term': 'Proteins', 'uri': 'http://edamontology.org/topic_0078'}, {'term': 'Sequence analysis', 'uri': 'http://edamontology.org/topic_0080'}, {'term': 'Protein sites, features and motifs', 'uri': 'http://edamontology.org/topic_3510'}]",[],1,[],False,False,[],"['Linux', 'Windows', 'Mac']",[],[],[],"[[['General'], 'http://compsysbio.org/subseqer/documentation.php']]",,False,False,['The Parkinson Lab'],[]
adgo,ADGO is a web tool that provides composite interpretations for microarray data comparing two sample groups. It also provides composite interpretations and enrichment analysis for lists of genes from diverse sources of biological information.,[],['Web application'],"[{'term': 'Microarray experiment', 'uri': 'http://edamontology.org/topic_3518'}, {'term': 'Gene expression', 'uri': 'http://edamontology.org/topic_0203'}, {'term': 'Sample collections', 'uri': 'http://edamontology.org/topic_3277'}, {'term': 'Sequence composition, complexity and repeats', 'uri': 'http://edamontology.org/topic_0157'}]",[],2,[],False,False,[],"['Linux', 'Windows', 'Mac']",[],[],[],"[[['General'], 'http://www.btool.org/ADGO2']]",,False,False,['ADGO Support'],[]
barcode generator,The program generates barcodes for sequences suitable for Illumina sequencing.,[],['Command-line tool'],"[{'term': 'Sequence composition, complexity and repeats', 'uri': 'http://edamontology.org/topic_0157'}, {'term': 'Sequencing', 'uri': 'http://edamontology.org/topic_3168'}, {'term': 'Data identity and mapping', 'uri': 'http://edamontology.org/topic_3345'}]",[],0,[],False,False,[],"['Linux', 'Windows', 'Mac']",[],[],[],"[[['General'], 'http://comailab.genomecenter.ucdavis.edu/index.php/Barcode_generator']]",,False,False,['Support'],[]
......@@ -152,7 +152,7 @@ geecee,Calculate fractional GC content of nucleic acid sequences.,['r6'],['Comma
compseq,Calculate the composition of unique words in sequences.,['r6'],['Command-line tool'],"[{'term': 'Sequence composition, complexity and repeats', 'uri': 'http://edamontology.org/topic_0157'}]","[{'url': 'http://emboss.open-bio.org/html/adm/ch01s01.html', 'note': None, 'type': ['Repository']}]",3,"[['Source code', 'http://emboss.open-bio.org/html/adm/ch01s01.html'], ['Binaries', 'http://emboss.open-bio.org/html/adm/ch01s01.html']]",False,False,['http://emboss.open-bio.org/html/adm/ch01s01.html'],"['Linux', 'Windows', 'Mac']","[{'data': {'term': 'sequence composition report', 'uri': 'http://edamontology.org/data_1261'}}]","[{'data': {'term': 'sequence composition report', 'uri': 'http://edamontology.org/data_1261'}}]",[],"[[['Terms of use'], 'http://emboss.open-bio.org/html/dev/ch01s01.html'], [['Citation instructions'], 'http://emboss.open-bio.org/html/use/pr02s04.html'], [['General'], 'http://emboss.open-bio.org/rel/rel6/apps/compseq.html']]",GPL-3.0,False,False,"['EMBOSS Contributors', 'EMBL-EBI', 'UK MRC', 'Wellcome Trust', 'UK BBSRC', 'EMBOSS']",['http://emboss.open-bio.org/html/adm/ch01s01.html']
chaos,Draw a chaos game representation plot for a nucleotide sequence.,['r6'],['Command-line tool'],"[{'term': 'Sequence composition, complexity and repeats', 'uri': 'http://edamontology.org/topic_0157'}]","[{'url': 'http://emboss.open-bio.org/html/adm/ch01s01.html', 'note': None, 'type': ['Repository']}]",3,"[['Source code', 'http://emboss.open-bio.org/html/adm/ch01s01.html'], ['Binaries', 'http://emboss.open-bio.org/html/adm/ch01s01.html']]",False,False,['http://emboss.open-bio.org/html/adm/ch01s01.html'],"['Linux', 'Windows', 'Mac']","[{'data': {'term': 'nucleic acid sequence record', 'uri': 'http://edamontology.org/data_2887'}}]","[{'data': {'term': 'nucleic acid sequence record', 'uri': 'http://edamontology.org/data_2887'}}]",[],"[[['Terms of use'], 'http://emboss.open-bio.org/html/dev/ch01s01.html'], [['Citation instructions'], 'http://emboss.open-bio.org/html/use/pr02s04.html'], [['General'], 'http://emboss.open-bio.org/rel/rel6/apps/chaos.html']]",GPL-3.0,False,False,"['EMBOSS Contributors', 'EMBL-EBI', 'UK MRC', 'Wellcome Trust', 'UK BBSRC', 'EMBOSS']",['http://emboss.open-bio.org/html/adm/ch01s01.html']
seqentropy,Assessmemt tool of sequence repeats for short read sequencing.,[],['Command-line tool'],"[{'term': 'Sequencing', 'uri': 'http://edamontology.org/topic_3168'}, {'term': 'DNA', 'uri': 'http://edamontology.org/topic_0654'}, {'term': 'Sequence composition, complexity and repeats', 'uri': 'http://edamontology.org/topic_0157'}, {'term': 'Genomics', 'uri': 'http://edamontology.org/topic_0622'}]","[{'url': 'http://www.mybiosoftware.com/seqentropy-2-0-1-assessmemt-tool-sequence-repeats-short-read-sequencing.html', 'note': None, 'type': ['Software catalogue']}]",1,[],False,False,[],"['Linux', 'Windows', 'Mac']",[],[],[],"[[['General'], 'https://sourceforge.net/projects/seqentropy/?source=navbar']]",,False,False,[],[]
sbars,A bioinformatics tool for searching of different types of long repeats in sequences comparable by size with chromosomes.,[],['Desktop application'],"[{'term': 'Sequencing', 'uri': 'http://edamontology.org/topic_3168'}, {'term': 'Sequence composition, complexity and repeats', 'uri': 'http://edamontology.org/topic_0157'}, {'term': 'DNA', 'uri': 'http://edamontology.org/topic_0654'}]","[{'url': 'http://www.mybiosoftware.com/sbars-spectral-based-approach-for-repeats-search.html', 'note': None, 'type': ['Software catalogue']}]",1,[],False,False,[],"['Linux', 'Windows']",[],[],[],"[[['User manual'], 'https://github.com/mpyatkov/sbars/raw/master/SBARS.pdf']]",,False,False,[],[]
sbars,A bioinformatics tool for searching of different types of long repeats in sequences comparable by size with chromosomes.,[],['Desktop application'],"[{'term': 'Sequencing', 'uri': 'http://edamontology.org/topic_3168'}, {'term': 'Sequence composition, complexity and repeats', 'uri': 'http://edamontology.org/topic_0157'}, {'term': 'DNA', 'uri': 'http://edamontology.org/topic_0654'}]","[{'url': 'http://www.mybiosoftware.com/sbars-spectral-based-approach-for-repeats-search.html', 'note': None, 'type': ['Software catalogue']}]",1,[],True,False,[],"['Linux', 'Windows']",[],[],[],"[[['User manual'], 'https://github.com/mpyatkov/sbars/raw/master/SBARS.pdf']]",,False,False,[],[]
equicktandem,Find tandem repeats in nucleotide sequences.,['r6'],['Command-line tool'],"[{'term': 'Sequence composition, complexity and repeats', 'uri': 'http://edamontology.org/topic_0157'}]","[{'url': 'http://emboss.open-bio.org/html/adm/ch01s01.html', 'note': None, 'type': ['Repository']}]",3,"[['Source code', 'http://emboss.open-bio.org/html/adm/ch01s01.html'], ['Binaries', 'http://emboss.open-bio.org/html/adm/ch01s01.html']]",False,False,['http://emboss.open-bio.org/html/adm/ch01s01.html'],"['Linux', 'Windows', 'Mac']","[{'data': {'term': 'nucleic acid sequence record', 'uri': 'http://edamontology.org/data_2887'}}]","[{'data': {'term': 'nucleic acid sequence record', 'uri': 'http://edamontology.org/data_2887'}}]",[],"[[['Terms of use'], 'http://emboss.open-bio.org/html/dev/ch01s01.html'], [['Citation instructions'], 'http://emboss.open-bio.org/html/use/pr02s04.html'], [['General'], 'http://emboss.open-bio.org/rel/rel6/apps/equicktandem.html']]",GPL-3.0,False,False,"['EMBOSS Contributors', 'EMBL-EBI', 'UK MRC', 'Wellcome Trust', 'UK BBSRC', 'EMBOSS']",['http://emboss.open-bio.org/html/adm/ch01s01.html']
genes by isoelectric point,Web service that retrieves all genes whose protein product has an isoelectric point in a range that user specify.,['1'],['Web API'],"[{'term': 'Sequence composition, complexity and repeats', 'uri': 'http://edamontology.org/topic_0157'}]","[{'url': 'https://www.biocatalogue.org/services/3406', 'note': None, 'type': ['Software catalogue']}]",0,[],False,False,[],"['Linux', 'Windows', 'Mac']",[],[],[],"[[['General'], 'http://mango.ctegd.uga.edu/jkissingLab/contact.html']]",,False,False,['BioCatalogue'],[]
mwcontam,Find weights common to multiple molecular weights files.,['r6'],['Command-line tool'],"[{'term': 'Sequence composition, complexity and repeats', 'uri': 'http://edamontology.org/topic_0157'}]","[{'url': 'http://emboss.open-bio.org/html/adm/ch01s01.html', 'note': None, 'type': ['Repository']}]",3,"[['Source code', 'http://emboss.open-bio.org/html/adm/ch01s01.html'], ['Binaries', 'http://emboss.open-bio.org/html/adm/ch01s01.html']]",False,False,['http://emboss.open-bio.org/html/adm/ch01s01.html'],"['Linux', 'Windows', 'Mac']","[{'data': {'term': 'amino acid index (molecular weight)', 'uri': 'http://edamontology.org/data_1505'}}]","[{'data': {'term': 'amino acid index (molecular weight)', 'uri': 'http://edamontology.org/data_1505'}}]",[],"[[['Terms of use'], 'http://emboss.open-bio.org/html/dev/ch01s01.html'], [['Citation instructions'], 'http://emboss.open-bio.org/html/use/pr02s04.html'], [['General'], 'http://emboss.open-bio.org/rel/rel6/apps/mwcontam.html']]",GPL-3.0,False,False,"['EMBOSS Contributors', 'EMBL-EBI', 'UK MRC', 'Wellcome Trust', 'UK BBSRC', 'EMBOSS']",['http://emboss.open-bio.org/html/adm/ch01s01.html']
......
......@@ -3,10 +3,10 @@ repeatmodeler,False,True,True,False,True,False,False,False,False,False,False,Fal
prigsa2,False,True,True,False,True,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False
popstr2,False,True,True,False,True,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False
nanosatellite,False,True,True,False,True,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,True,False
tricolor,True,True,True,True,False,False,True,False,False,True,True,False,False,False,True,True,True,False,False,False,True,False,False,True,True
repet,True,True,True,True,True,False,True,False,False,True,True,True,False,False,True,True,True,False,False,False,True,False,False,True,False
tricolor,True,True,True,True,False,False,True,True,False,True,True,False,False,False,True,True,True,False,False,False,True,False,False,True,True
repet,True,True,True,True,True,False,True,True,False,True,True,True,False,False,True,True,True,False,False,False,True,False,False,True,False
kmasker,True,True,True,True,True,False,False,False,False,False,False,False,False,False,True,True,True,False,False,False,True,False,False,True,True
kmasker,True,True,True,True,True,False,True,False,False,False,True,True,False,False,True,True,True,False,False,False,True,False,False,True,True
kmasker,True,True,True,True,True,False,True,True,False,False,True,True,False,False,True,True,True,False,False,False,True,False,False,True,True
ostrfpd,False,True,True,False,True,False,False,False,False,False,True,True,False,False,False,False,False,False,False,False,True,False,False,True,False
ultra,False,True,True,False,True,False,False,False,False,False,True,True,False,False,False,False,False,False,False,False,True,False,False,True,False
pipealign2,False,True,True,False,True,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False
......@@ -45,8 +45,8 @@ interpro,False,True,True,False,True,False,False,False,False,False,False,False,Fa
pfam,False,True,True,False,True,True,False,False,False,False,False,False,False,False,False,False,False,True,False,False,True,False,False,True,False
repeatsdb,True,True,True,False,True,False,False,False,False,False,False,False,False,False,False,False,False,True,False,False,True,False,False,True,False
reputer,False,True,True,True,True,True,False,False,False,False,False,False,False,False,True,True,True,True,False,False,True,False,False,True,False
reputer,False,True,True,True,True,False,True,False,False,True,True,True,False,False,True,True,True,True,False,False,True,False,False,True,False
radar,False,True,True,False,True,True,False,False,False,False,False,False,False,False,False,False,False,False,False,False,True,True,False,True,False
reputer,False,True,True,True,True,False,True,True,False,True,True,True,False,False,True,True,True,True,False,False,True,False,False,True,False
radar,False,True,True,False,True,True,False,False,False,False,False,False,False,False,False,False,False,False,False,False,True,True,True,True,False
trdistiller,False,True,True,False,True,False,False,False,False,False,True,True,False,False,False,False,False,False,False,False,True,False,False,False,False
gcat,True,True,True,False,True,False,False,False,False,False,True,True,False,False,False,False,False,False,False,False,True,False,False,False,False
kmer-ssr,False,True,True,False,True,False,False,False,False,False,True,False,False,False,False,False,False,False,False,False,True,False,False,True,False
......@@ -56,7 +56,7 @@ vivaxgen,False,True,True,False,True,False,False,False,False,False,False,False,Fa
lrrsearch,False,True,True,False,True,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,True,False,False,True,False
detectir,False,True,True,False,True,False,True,False,False,True,True,True,False,False,False,False,False,False,False,False,True,False,False,True,False
esap plus,False,True,True,False,True,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,True,False
spotyping,True,True,True,False,True,False,False,False,False,False,True,True,False,False,False,False,False,False,False,False,True,False,False,True,False
spotyping,True,True,True,False,True,False,False,True,False,False,True,True,False,False,False,False,False,False,False,False,True,False,False,True,False
sewer,False,True,True,False,True,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,True,False
gream,False,True,True,False,True,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,True,False,False,True,False
mreps,False,True,True,False,True,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,True,False,False,True,False
......@@ -87,7 +87,7 @@ protinfo ppc,False,True,True,False,True,False,False,False,False,False,False,Fals
repeatoire,False,True,True,False,True,False,False,False,False,False,True,True,False,False,False,False,False,False,False,False,True,False,False,False,False
eslpred,False,True,True,False,True,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,True,False,False,True,False
strap,False,True,True,False,True,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,True,False,False,True,False
genebreak,True,True,True,False,True,False,True,False,False,True,True,True,False,False,False,False,True,True,False,False,True,False,False,True,False
genebreak,True,True,True,False,True,False,True,True,False,True,True,True,False,False,False,False,True,True,False,False,True,False,False,True,False
subseqer,False,True,True,False,True,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,True,False,False,True,False
adgo,False,True,True,False,True,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,True,False,False,True,False
barcode generator,False,True,True,False,False,False,False,False,False,False,True,True,False,False,False,False,False,False,False,False,True,False,False,True,False
......@@ -101,41 +101,41 @@ pbil,False,True,True,False,True,False,False,False,False,False,False,False,False,
uniqueprot,False,True,True,False,True,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,True,False,False,True,False
rjprimers,False,True,True,False,True,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,True,False,False,True,False
tmsoc,False,True,True,False,True,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,True,False,False,True,False
oddcomp,False,True,True,True,True,False,True,False,False,True,True,True,False,False,False,False,False,False,False,False,True,False,False,True,False
palindrome,False,True,True,True,True,False,True,False,False,True,True,True,False,False,False,False,False,False,False,False,True,False,False,True,False
cpgreport,False,True,True,True,True,False,True,False,False,True,True,True,False,False,False,False,False,False,False,False,True,False,False,True,False
newcpgreport,False,True,True,True,True,False,True,False,False,True,True,True,False,False,False,False,False,False,False,False,True,False,False,True,False
freak,False,True,True,True,True,False,True,False,False,True,True,True,False,False,False,False,False,False,False,False,True,False,False,True,False
density,False,True,True,True,True,False,True,False,False,True,True,True,False,False,False,False,False,False,False,False,True,False,False,True,False
geecee,False,True,True,True,True,False,True,False,False,True,True,True,False,False,False,False,False,False,False,False,True,False,False,True,False
compseq,False,True,True,True,True,False,True,False,False,True,True,True,False,False,False,False,False,False,False,False,True,False,False,True,False
chaos,False,True,True,True,True,False,True,False,False,True,True,True,False,False,False,False,False,False,False,False,True,False,False,True,False
oddcomp,False,True,True,True,True,False,True,False,False,True,True,True,False,False,False,False,False,False,False,False,True,False,True,True,False
palindrome,False,True,True,True,True,False,True,False,False,True,True,True,False,False,False,False,False,False,False,False,True,False,True,True,False
cpgreport,False,True,True,True,True,False,True,False,False,True,True,True,False,False,False,False,False,False,False,False,True,False,True,True,False
newcpgreport,False,True,True,True,True,False,True,False,False,True,True,True,False,False,False,False,False,False,False,False,True,False,True,True,False
freak,False,True,True,True,True,False,True,False,False,True,True,True,False,False,False,False,False,False,False,False,True,False,True,True,False
density,False,True,True,True,True,False,True,False,False,True,True,True,False,False,False,False,False,False,False,False,True,False,True,True,False
geecee,False,True,True,True,True,False,True,False,False,True,True,True,False,False,False,False,False,False,False,False,True,False,True,True,False
compseq,False,True,True,True,True,False,True,False,False,True,True,True,False,False,False,False,False,False,False,False,True,False,True,True,False
chaos,False,True,True,True,True,False,True,False,False,True,True,True,False,False,False,False,False,False,False,False,True,False,True,True,False
seqentropy,False,True,True,False,True,False,False,False,False,False,True,True,False,False,False,False,False,False,False,False,True,False,False,False,False
sbars,False,True,True,False,True,False,False,False,False,False,True,True,False,False,False,False,False,False,False,False,True,False,False,False,False
equicktandem,False,True,True,True,True,False,True,False,False,True,True,True,False,False,False,False,False,False,False,False,True,False,False,True,False
sbars,False,True,True,False,True,False,False,True,False,False,True,True,False,False,False,False,False,False,False,False,True,False,False,False,False
equicktandem,False,True,True,True,True,False,True,False,False,True,True,True,False,False,False,False,False,False,False,False,True,False,True,True,False
genes by isoelectric point,False,True,True,False,False,False,False,False,False,False,False,False,False,False,False,False,False,True,False,False,True,False,False,True,False
mwcontam,False,True,True,True,True,False,True,False,False,True,True,True,False,False,False,False,False,False,False,False,True,False,False,True,False
wordcount,False,True,True,True,True,False,True,False,False,True,True,True,False,False,False,False,False,False,False,False,True,False,False,True,False
emowse,False,True,True,True,True,False,True,False,False,True,True,True,False,False,False,False,False,False,False,False,True,False,False,True,False
etandem,False,True,True,True,True,False,True,False,False,True,True,True,False,False,False,False,False,False,False,False,True,False,False,True,False
iva,False,True,True,False,True,False,False,False,False,False,True,False,False,False,False,False,False,False,False,False,False,False,False,False,False
newcpgseek,False,True,True,True,True,False,True,False,False,True,True,True,False,False,False,False,False,False,False,False,True,False,False,True,False
mwcontam,False,True,True,True,True,False,True,False,False,True,True,True,False,False,False,False,False,False,False,False,True,False,True,True,False
wordcount,False,True,True,True,True,False,True,False,False,True,True,True,False,False,False,False,False,False,False,False,True,False,True,True,False
emowse,False,True,True,True,True,False,True,False,False,True,True,True,False,False,False,False,False,False,False,False,True,False,True,True,False
etandem,False,True,True,True,True,False,True,False,False,True,True,True,False,False,False,False,False,False,False,False,True,False,True,True,False
iva,False,True,True,False,True,False,False,False,False,False,True,False,False,False,False,False,False,False,False,False,False,False,True,False,False
newcpgseek,False,True,True,True,True,False,True,False,False,True,True,True,False,False,False,False,False,False,False,False,True,False,True,True,False
trust,False,True,True,False,True,True,False,False,False,False,False,False,False,False,False,False,False,False,False,False,True,False,False,False,False
peptide match,False,True,True,False,True,False,False,False,False,False,False,False,False,False,False,False,False,True,False,False,True,False,False,True,False
mwfilter,False,True,True,True,True,False,True,False,False,True,True,True,False,False,False,False,False,False,False,False,True,False,False,True,False
mwfilter,False,True,True,True,True,False,True,False,False,True,True,True,False,False,False,False,False,False,False,False,True,False,True,True,False
repdenovo,False,True,True,False,True,False,False,False,False,False,True,True,False,False,False,False,False,False,False,False,True,False,False,False,False
cpgplot,False,True,True,True,True,False,True,False,False,True,True,True,False,False,False,False,False,False,False,False,True,False,False,True,False
isochore,False,True,True,True,True,False,True,False,False,True,True,True,False,False,False,False,False,False,False,False,True,False,False,True,False
einverted,False,True,True,True,True,False,True,False,False,True,True,True,False,False,False,False,False,False,False,False,True,False,False,True,False
cpgplot,False,True,True,True,True,False,True,False,False,True,True,True,False,False,False,False,False,False,False,False,True,False,True,True,False
isochore,False,True,True,True,True,False,True,False,False,True,True,True,False,False,False,False,False,False,False,False,True,False,True,True,False
einverted,False,True,True,True,True,False,True,False,False,True,True,True,False,False,False,False,False,False,False,False,True,False,True,True,False
pssrdb,False,True,True,False,True,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,True,False
lalign,False,True,True,False,True,True,False,False,False,False,False,False,False,False,False,False,False,False,False,False,True,True,False,True,False
censor,False,True,True,False,True,True,False,False,False,False,False,False,False,False,False,False,False,False,False,False,True,True,False,True,False
lalign,False,True,True,False,True,True,False,False,False,False,False,False,False,False,False,False,False,False,False,False,True,True,True,True,False
censor,False,True,True,False,True,True,False,False,False,False,False,False,False,False,False,False,False,False,False,False,True,True,True,True,False
satellog,False,True,True,False,True,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,True,False,False,True,False
newcpgreport (ebi),False,True,True,False,True,True,False,False,False,False,False,False,False,False,False,False,False,False,False,False,True,True,False,True,False
cpgplot (ebi),False,True,True,False,True,True,False,False,False,False,False,False,False,False,False,False,False,False,False,False,True,True,False,True,False
newcpgreport (ebi),False,True,True,False,True,True,False,False,False,False,False,False,False,False,False,False,False,False,False,False,True,True,True,True,False
cpgplot (ebi),False,True,True,False,True,True,False,False,False,False,False,False,False,False,False,False,False,False,False,False,True,True,True,True,False
polyq,False,True,True,False,True,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,True,False,False,True,False
tral,False,True,True,False,True,False,False,False,False,False,True,True,False,False,False,False,False,True,False,False,True,False,False,True,False
isochore (ebi),False,True,True,False,True,True,False,False,False,False,False,False,False,False,False,False,False,False,False,False,True,True,False,True,False
isochore (ebi),False,True,True,False,True,True,False,False,False,False,False,False,False,False,False,False,False,False,False,False,True,True,True,True,False
reupred,False,True,True,False,True,False,False,False,False,False,True,True,False,False,False,False,False,True,False,False,True,False,False,False,False
trap,False,True,True,False,True,False,False,False,False,False,True,True,False,False,False,False,False,False,False,False,True,False,False,False,False
vntrfinder,False,True,True,False,True,False,False,False,False,False,True,True,False,False,False,False,False,False,False,False,True,False,False,False,False
......
......@@ -3,10 +3,10 @@ repeatmodeler,0.54,0.0,0.0,0.0,0.135
prigsa2,0.54,0.0,0.0,0.0,0.135
popstr2,0.54,0.0,0.0,0.0,0.135
nanosatellite,0.54,0.0,0.0,0.2,0.185
tricolor,0.9400000000000002,0.565,0.6,0.7,0.7012499999999999
repet,1.0,0.6399999999999999,0.6,0.5,0.6849999999999999
tricolor,0.9400000000000002,0.7049999999999998,0.6,0.7,0.7362500000000001
repet,1.0,0.7799999999999999,0.6,0.5,0.72
kmasker,1.0,0.0,0.6,0.7,0.575
kmasker,1.0,0.5,0.6,0.7,0.7
kmasker,1.0,0.6399999999999999,0.6,0.7,0.7349999999999999
ostrfpd,0.54,0.15,0.0,0.5,0.2975
ultra,0.54,0.15,0.0,0.5,0.2975
pipealign2,0.54,0.0,0.0,0.0,0.135
......@@ -45,7 +45,7 @@ interpro,0.54,0.0,0.0,0.5,0.26
pfam,0.54,0.42,0.1,0.5,0.39
repeatsdb,0.9400000000000002,0.0,0.1,0.5,0.38500000000000006
reputer,0.6000000000000001,0.42,0.7,0.5,0.5549999999999999
reputer,0.6000000000000001,0.6399999999999999,0.7,0.5,0.61
reputer,0.6000000000000001,0.7799999999999999,0.7,0.5,0.645
radar,0.54,0.42,0.0,0.8,0.44
trdistiller,0.54,0.15,0.0,0.3,0.2475
gcat,0.9400000000000002,0.15,0.0,0.3,0.34750000000000003
......@@ -56,7 +56,7 @@ vivaxgen,0.54,0.0,0.0,0.5,0.26
lrrsearch,0.54,0.0,0.0,0.5,0.26
detectir,0.54,0.6399999999999999,0.0,0.5,0.42
esap plus,0.54,0.0,0.0,0.2,0.185
spotyping,0.9400000000000002,0.15,0.0,0.5,0.3975
spotyping,0.9400000000000002,0.29,0.0,0.5,0.43250000000000005
sewer,0.54,0.0,0.0,0.2,0.185
gream,0.54,0.0,0.0,0.5,0.26
mreps,0.54,0.0,0.0,0.5,0.26
......@@ -87,7 +87,7 @@ protinfo ppc,0.54,0.0,0.0,0.5,0.26
repeatoire,0.54,0.15,0.0,0.3,0.2475
eslpred,0.54,0.0,0.0,0.5,0.26
strap,0.54,0.0,0.0,0.5,0.26
genebreak,0.9400000000000002,0.6399999999999999,0.22,0.5,0.575
genebreak,0.9400000000000002,0.7799999999999999,0.22,0.5,0.6100000000000001
subseqer,0.54,0.0,0.0,0.5,0.26
adgo,0.54,0.0,0.0,0.5,0.26
barcode generator,0.48,0.15,0.0,0.5,0.2825
......@@ -101,32 +101,32 @@ pbil,0.54,0.0,0.0,0.5,0.26
uniqueprot,0.54,0.0,0.0,0.5,0.26
rjprimers,0.54,0.0,0.0,0.5,0.26
tmsoc,0.54,0.0,0.0,0.5,0.26
oddcomp,0.6000000000000001,0.6399999999999999,0.0,0.5,0.435
palindrome,0.6000000000000001,0.6399999999999999,0.0,0.5,0.435
cpgreport,0.6000000000000001,0.6399999999999999,0.0,0.5,0.435
newcpgreport,0.6000000000000001,0.6399999999999999,0.0,0.5,0.435
freak,0.6000000000000001,0.6399999999999999,0.0,0.5,0.435
density,0.6000000000000001,0.6399999999999999,0.0,0.5,0.435
geecee,0.6000000000000001,0.6399999999999999,0.0,0.5,0.435
compseq,0.6000000000000001,0.6399999999999999,0.0,0.5,0.435
chaos,0.6000000000000001,0.6399999999999999,0.0,0.5,0.435
oddcomp,0.6000000000000001,0.6399999999999999,0.0,0.8,0.51
palindrome,0.6000000000000001,0.6399999999999999,0.0,0.8,0.51
cpgreport,0.6000000000000001,0.6399999999999999,0.0,0.8,0.51
newcpgreport,0.6000000000000001,0.6399999999999999,0.0,0.8,0.51
freak,0.6000000000000001,0.6399999999999999,0.0,0.8,0.51
density,0.6000000000000001,0.6399999999999999,0.0,0.8,0.51
geecee,0.6000000000000001,0.6399999999999999,0.0,0.8,0.51
compseq,0.6000000000000001,0.6399999999999999,0.0,0.8,0.51
chaos,0.6000000000000001,0.6399999999999999,0.0,0.8,0.51
seqentropy,0.54,0.15,0.0,0.3,0.2475
sbars,0.54,0.15,0.0,0.3,0.2475
equicktandem,0.6000000000000001,0.6399999999999999,0.0,0.5,0.435
sbars,0.54,0.29,0.0,0.3,0.28250000000000003
equicktandem,0.6000000000000001,0.6399999999999999,0.0,0.8,0.51
genes by isoelectric point,0.48,0.0,0.1,0.5,0.27
mwcontam,0.6000000000000001,0.6399999999999999,0.0,0.5,0.435
wordcount,0.6000000000000001,0.6399999999999999,0.0,0.5,0.435
emowse,0.6000000000000001,0.6399999999999999,0.0,0.5,0.435
etandem,0.6000000000000001,0.6399999999999999,0.0,0.5,0.435
iva,0.54,0.075,0.0,0.0,0.15375
newcpgseek,0.6000000000000001,0.6399999999999999,0.0,0.5,0.435
mwcontam,0.6000000000000001,0.6399999999999999,0.0,0.8,0.51
wordcount,0.6000000000000001,0.6399999999999999,0.0,0.8,0.51
emowse,0.6000000000000001,0.6399999999999999,0.0,0.8,0.51
etandem,0.6000000000000001,0.6399999999999999,0.0,0.8,0.51
iva,0.54,0.075,0.0,0.3,0.22875
newcpgseek,0.6000000000000001,0.6399999999999999,0.0,0.8,0.51
trust,0.54,0.42,0.0,0.3,0.315
peptide match,0.54,0.0,0.1,0.5,0.28500000000000003
mwfilter,0.6000000000000001,0.6399999999999999,0.0,0.5,0.435
mwfilter,0.6000000000000001,0.6399999999999999,0.0,0.8,0.51
repdenovo,0.54,0.15,0.0,0.3,0.2475
cpgplot,0.6000000000000001,0.6399999999999999,0.0,0.5,0.435
isochore,0.6000000000000001,0.6399999999999999,0.0,0.5,0.435
einverted,0.6000000000000001,0.6399999999999999,0.0,0.5,0.435
cpgplot,0.6000000000000001,0.6399999999999999,0.0,0.8,0.51
isochore,0.6000000000000001,0.6399999999999999,0.0,0.8,0.51
einverted,0.6000000000000001,0.6399999999999999,0.0,0.8,0.51
pssrdb,0.54,0.0,0.0,0.2,0.185
lalign,0.54,0.42,0.0,0.8,0.44
censor,0.54,0.42,0.0,0.8,0.44
......
......@@ -4,6 +4,9 @@ import yaml
import sys
global webTypes
webTypes = ['Web API', 'Web application', 'Web service', 'Suite', 'Workbench', 'Database portal']
def prepFAIRcomp(instances):
global stdFormats
......@@ -129,8 +132,6 @@ class instance(object):
##============== Accessibility metrics computation functions ================
global webTypes
webTypes = ['Web API', 'Web application', 'Web service', 'Suite', 'Workbench', 'Database portal']
def compA1_1(self):
'''
WEB
......@@ -252,8 +253,9 @@ class instance(object):
if self.super_type == 'no_web':
eInfra = ['vre.multiscalegenomics.eu', 'galaxy.', 'usegalaxy.']
for url in self.links:
if True in [a in url for a in eInfra]:
return(True)
for e in eInfra:
if e in url['url']:
return(True)
else:
return(False)
return(False)
......@@ -268,11 +270,12 @@ class instance(object):
Whether the software can be used in several e-infrastructure
'''
if self.super_type == 'no_web':
eInfra = ['vre.multiscalegenomics.eu', 'galaxy.', 'usegalaxy.']
count = 0
eInfra = ['vre.multiscalegenomics.eu', 'galaxy.', 'usegalaxy.']
for url in self.links:
if True in [a in url for a in eInfra]:
count += 1
for e in eInfra:
if e in url['url']:
count += 1
if count>1:
return(True)
......@@ -424,6 +427,8 @@ class instance(object):
for doc in self.documentation:
if doc[0][0].lower() == 'conditions of use':
return(True)
if doc[0][0].lower() == 'terms of use':
return(True)
return(False)
......@@ -509,7 +514,7 @@ class instance(object):
self.metrics.A3_2 = self.compA3_2()
self.metrics.A3_3 = self.compA3_3()
self.metrics.A3_4 = self.compA3_4()
self.metrics.A3_5 = self.compA3_4()
self.metrics.A3_5 = self.compA3_5()
self.metrics.I1_1 = self.compI1_1() # TO DO
#self.metrics.I1_2 = False # NOT FOR NOW
......@@ -531,6 +536,7 @@ class instance(object):
self.metrics.R2_2 = self.compR2_2()
#self.metrics.R3_1 = False # Not for now
self.metrics.R3_2 = self.compR3_2()
self.metrics.R4_1 = self.compR4_1()
......@@ -738,8 +744,9 @@ class biotoolsToolsGenerator(toolGenerator):
return(doc)
def parse_install_instr(self, tool, newInst):
if 'Manual' in [ doc[0] for doc in newInst.documentation ]:
return(True)
for d in newInst.documentation:
if 'manual' in d[0][0].lower():
return(True)
else:
return(False)
......
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