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cath_tools [2016/08/02 12:23]
sillitoe 		cath_tools [2017/10/16 14:39] (current)
sayoni [Pipeline] Added scorecons
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-====== CATH Tools ======+====== Open Source Software ======
  
-This page aims to acknowledge the open source software projects that have been contributed to this resource and web site. +This page aims to acknowledge the open source software projects that have been contributed to this resource. 
  
-==== Web application ====+===== CATH Tools ===== 
 + 
 +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 
 + 
 +===== 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 =====
 +
 +  * [[ 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://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 
  
  

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