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cath_tools [2016/08/02 12:31] – sillitoecath_tools [2017/10/16 14:39] (current) – [Pipeline] Added scorecons sayoni
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 This page aims to acknowledge the open source software projects that have been contributed to this resource.  This page aims to acknowledge the open source software projects that have been contributed to this resource. 
  
-==== CATH Tools ====+===== CATH Tools =====
  
-CATH open source software is being developed under the [[ https://github.com/UCLOrengoGroup | @UCLOrengoGroup ]] on GitHub.+Our own open source software is being developed as [[ https://github.com/UCLOrengoGroup | @UCLOrengoGroup ]] on GitHub.
  
   * [[ https://github.com/UCLOrengoGroup/cath-tools | cath-tools]] -- Protein structure comparison tools   * [[ https://github.com/UCLOrengoGroup/cath-tools | cath-tools]] -- Protein structure comparison tools
  
-==== Web application ====+===== Web application =====
  
   * [[ https://www.perl.org | Perl ]] -- The Perl Programming Language    * [[ https://www.perl.org | Perl ]] -- The Perl Programming Language 
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   * [[ https://bioperl.org | BioPerl ]] -- Perl tools for bioinformatics, genomics and life science   * [[ https://bioperl.org | BioPerl ]] -- Perl tools for bioinformatics, genomics and life science
  
-==== Web deployment/architecture ====+===== Web deployment/architecture =====
  
   * [[ https://varnish-cache.org | Varnish Cache ]] -- Web application accelerator   * [[ https://varnish-cache.org | Varnish Cache ]] -- Web application accelerator
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   * [[ http://lucene.apache.org/solr/| Apache Solr ]] -- Enterprise Search Platform   * [[ http://lucene.apache.org/solr/| Apache Solr ]] -- Enterprise Search Platform
  
-==== Web pages ====+===== Web pages =====
  
-  * [[https://github.com/wilzbach/msa | MSAViewer ]] -- Multiple Sequence Alignment Viewer ([[https://github.com/wilzbach/msa | @wilzbach]]) ((Guy Yachdav, Sebastian Wilzbach, Benedikt Rauscher, Robert Sheridan, Ian Sillitoe, James Procter, Suzanna Lewis, Burkhard Rost, Tatyana Goldberg. "MSAViewer: interactive JavaScript visualization of multiple sequence alignments." Bioinformatics (2016) )) +  * [[https://github.com/wilzbach/msa | MSAViewer ]] -- Multiple Sequence Alignment Viewer (thanks [[https://github.com/wilzbach | @wilzbach]]) ((Guy Yachdav, Sebastian Wilzbach, Benedikt Rauscher, Robert Sheridan, Ian Sillitoe, James Procter, Suzanna Lewis, Burkhard Rost, Tatyana Goldberg. [[ http://doi.org/10.1093/bioinformatics/btw474 | "MSAViewer: interactive JavaScript visualization of multiple sequence alignments." ]] Bioinformatics (2016) )) 
-  * [[https://github.com/3dmol/3Dmol.js | 3Dmol.js ]] -- A modern, object-oriented JavaScript library for visualizing molecular data (( Nicholas Rego and David Koes 3Dmol.js: molecular visualization with WebGL Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829 ))+  * [[https://github.com/3dmol/3Dmol.js | 3Dmol.js ]] -- A modern, object-oriented JavaScript library for visualizing molecular data (( Nicholas Rego and David Koes [[ http://doi.org/10.1093/bioinformatics/btu829 | 3Dmol.js: molecular visualization with WebGL Bioinformatics ]] (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829 ))
   * [[https://d3js.org/ | D3 ]] -- Data-Driven Documents   * [[https://d3js.org/ | D3 ]] -- Data-Driven Documents
   * [[https://biojs.net BioJS | BioJS ]] -- Modern data visualizations for the web   * [[https://biojs.net BioJS | BioJS ]] -- Modern data visualizations for the web
  
-==== Pipeline ====+===== Pipeline =====
  
   * [[ http://blast.ncbi.nlm.nih.gov/Blast.cgi | BLAST ]] -- Basic Local Alignment Search Tool   * [[ http://blast.ncbi.nlm.nih.gov/Blast.cgi | BLAST ]] -- Basic Local Alignment Search Tool
-  * [[ http://hmmer.org | HMMER3 ]] -- Biosequence analysis using profile hidden Markov models+  * [[ http://hmmer.org | HMMER3 ]] -- Biosequence analysis using profile Hidden Markov Models
   * [[ http://mafft.cbrc.jp/alignment/software/ | MAFFT ]] -- Multiple alignment program   * [[ http://mafft.cbrc.jp/alignment/software/ | MAFFT ]] -- Multiple alignment program
 +  * [[ https://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/valdar/scorecons_server.pl | Scorecons ]] -- Scores residue conservation in a multiple sequence alignment 
  
  
cath_tools.1470141110.txt.gz · Last modified: by sillitoe

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