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

Bioinformatics
Alexandre PoliakovInna Dubchak

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. 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/.

References

Apr 26, 2000·Genome Research·S SchwartzW Miller
Apr 5, 2002·Genome Research·W James Kent
Jan 17, 2003·Genome Research·Nick BrayLior Pachter
Mar 26, 2003·Genome Research·Michael BrudnoSerafim Batzoglou
Jul 12, 2003·Bioinformatics·Michael BrudnoSerafim Batzoglou
Dec 19, 2003·Nucleic Acids Research·Karsten Suhre, Jean-Michel Claverie
Jun 25, 2004·Nucleic Acids Research·Kelly A FrazerInna Dubchak
Jun 28, 2005·Nucleic Acids Research·Gabriela G Loots, Ivan Ovcharenko
Jan 30, 2009·Genome Research·Inna DubchakMichael Brudno
May 25, 2010·Nature Biotechnology·Xiaoyu Chen, Martin Tompa
Aug 31, 2011·Genome Research·Chris P Ponting, Ross C Hardison
Nov 15, 2011·Nucleic Acids Research·Patricia P ChanTodd M Lowe

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Citations

Feb 21, 2016·Database : the Journal of Biological Databases and Curation·Javier HerreroPaul Flicek
Oct 24, 2017·Nucleic Acids Research·Sònia CasillasAntonio Barbadilla
Jan 18, 2018·BMC Genomics·Christine JandrasitsBernhard Y Renard
Oct 12, 2019·NPJ Systems Biology and Applications·Bede P BusbyPaul H Atkinson
Nov 16, 2019·Scientific Reports·Marko Premzl
Feb 26, 2020·Development, Growth & Differentiation·Nanoka Suzuki, Haruki Ochi
May 1, 2018·Frontiers in Plant Science·Fei ChenLiangsheng Zhang
Apr 4, 2020·NPJ Systems Biology and Applications·Bede P BusbyPaul H Atkinson
Oct 16, 2020·General and Comparative Endocrinology·Yann GuiguenJulien Bobe

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