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Table of Contents

CATH Tools

This page aims to acknowledge the open source software projects that have been contributed to this resource and web site.

Web application

  • Perl – The Perl Programming Language
  • Catalyst – MVC web application framework
  • Moose – Object system for Perl 5
  • DBIx::Class – Object relational mapper
  • BioPerl – Perl tools for bioinformatics, genomics and life science

Web deployment/architecture

Web pages

  • MSAViewer – Multiple Sequence Alignment Viewer ( @wilzbach) 1)
  • 3Dmol.js – A modern, object-oriented JavaScript library for visualizing molecular data 2)
  • D3 – Data-Driven Documents
  • BioJS – Modern data visualizations for the web

Pipeline

* BLAST – Basic Local Alignment Search Tool * HMMER3 – Biosequence analysis using profile hidden Markov models * MAFFT – Multiple alignment program for amino acid or nucleotide sequences

1) 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)
2) Nicholas Rego and David Koes 3Dmol.js: molecular visualization with WebGL Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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