Performs reference-assisted and de novo gene prediction, homolog protein family assignment, ortholog prediction, functional annotation, and pan-genome analysis. DeNoGAP integrates bioinformatics tools and databases for comparative analysis of a large number of Genomes. It scales linearly since the homology assignment is based on iteratively refined hidden Markov models. The pipeline offers tools and algorithms for annotation and analysis of completed and draft genome sequences.

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DeNoGAP specifications

Software type:
Pipeline
Restrictions to use:
None
Programming languages:
Perl, BioPerl
License:
GNU General Public License version 3.0
Version:
1.0
Requirements:
Apache
Source code URL:
https://sourceforge.net/p/denogap/code/ref/master/
Interface:
Command line interface
Operating system:
Unix/Linux
Database management system:
SQLite
Computer skills:
Advanced
Stability:
Stable

Publications

  • (Thakur and Guttman, 2016) A De-Novo Genome Analysis Pipeline (DeNoGAP) for large-scale comparative prokaryotic genomics studies. BMC Bioinformatics.
    PMID: 27363390

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Documentation

Credits

Institution(s)

Department of Cell & Systems Biology, University of Toronto, Toronto, ON, Canada; Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, Canada

Funding source(s)

This work was support by a grant from the Natural Sciences & Engineering Research Council of Canada and a Canada Research Chair.

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