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cath_tools [2016/08/02 12:25] 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 | ||
| Line 11: | Line 17: | ||
| * [[ 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 | ||
| Line 17: | Line 23: | ||
| * [[ 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 for amino acid or nucleotide sequences | + | * [[ 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 | ||
