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Bioinformatics DOI:10.1093/bioinformatics/btl193

Combo: a whole genome comparative browser.

Publication TypeJournal Article
Year of Publication2006
AuthorsEngels, R, Yu, T, Burge, C, Mesirov, JP, DeCaprio, D, Galagan, JE
JournalBioinformatics
Volume22
Issue14
Pages1782-3
Date Published2006 Jul 15
ISSN1367-4811
KeywordsAlgorithms, Base Sequence, Chromosome Mapping, Computer Graphics, Database Management Systems, Databases, Genetic, Information Storage and Retrieval, Molecular Sequence Data, Sequence Alignment, Sequence Analysis, DNA, Software, User-Computer Interface
Abstract

SUMMARY: Combo is a comparative genome browser that provides a dynamic view of whole genome alignments along with their associated annotations. Combo provides two different visualization perspectives. The perpendicular (dot plot) view provides a dot plot of genome alignments synchronized with a display of genome annotations along each axis. The parallel view displays two genome annotations horizontally, synchronized through a panel displaying local alignments as trapezoids. Users can zoom to any resolution, from whole chromosomes to individual bases. They can select, highlight and view detailed information from specific alignments and annotations. Combo is an organism agnostic and can import data from a variety of file formats.

AVAILABILITY: Combo is integrated as part of the Argo Genome Browser which also provides single-genome browsing and editing capabilities. Argo is written in Java, runs on multiple platforms and is freely available for download at http://www.broad.mit.edu/annotation/argo/.

URLhttp://bioinformatics.oxfordjournals.org/cgi/pmidlookup?view=long&pmid=16709588
DOI10.1093/bioinformatics/btl193
Pubmed

http://www.ncbi.nlm.nih.gov/pubmed/16709588?dopt=Abstract

Alternate JournalBioinformatics
PubMed ID16709588