GenomeVISTA--an integrated software package for whole-genome alignment and visualization

Alexandre Poliakov; Justin Foong; Michael Brudno; Inna Dubchak

doi:10.1093/bioinformatics/btu355

GenomeVISTA--an integrated software package for whole-genome alignment and visualization

Bioinformatics. 2014 Sep 15;30(18):2654-5. doi: 10.1093/bioinformatics/btu355. Epub 2014 May 23.

Authors

Alexandre Poliakov¹, Justin Foong¹, Michael Brudno², Inna Dubchak²

Affiliations

¹ US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA, Centre for Computational Medicine, Hospital for Sick Children, Toronto, ON M5G 1X8 Canada, Department of Computer Science, University of Toronto, Toronto, ON M5S 3G4 Canada and Genomics Division, LBNL, Berkeley, CA 94720, USA.
² US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA, Centre for Computational Medicine, Hospital for Sick Children, Toronto, ON M5G 1X8 Canada, Department of Computer Science, University of Toronto, Toronto, ON M5S 3G4 Canada and Genomics Division, LBNL, Berkeley, CA 94720, USA US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA, Centre for Computational Medicine, Hospital for Sick Children, Toronto, ON M5G 1X8 Canada, Department of Computer Science, University of Toronto, Toronto, ON M5S 3G4 Canada and Genomics Division, LBNL, Berkeley, CA 94720, USA.

Abstract

With the ubiquitous generation of complete genome assemblies for a variety of species, efficient tools for whole-genome alignment along with user-friendly visualization are critically important. Our VISTA family of tools for comparative genomics, based on algorithms for pairwise and multiple alignments of genomic sequences and whole-genome assemblies, has become one of the standard techniques for comparative analysis. Most of the VISTA programs have been implemented as Web-accessible servers and are extensively used by the biomedical community. In this manuscript, we introduce GenomeVISTA: a novel implementation that incorporates most features of the VISTA family--fast and accurate alignment, visualization capabilities, GUI and analytical tools within a stand-alone software package. GenomeVISTA thus provides flexibility and security for users who need to conduct whole-genome comparisons on their own computers.

Availability and implementation: Implemented in Perl, C/C++ and Java, the source code is freely available for download at the VISTA Web site: http://genome.lbl.gov/vista/.

Publication types

Research Support, N.I.H., Extramural
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Algorithms
Computer Graphics
Genomics / methods*
Sequence Alignment / methods*
Software*

Abstract

Publication types

MeSH terms

Grants and funding