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PMID: 15215394 Published · ppublish English Journal Article

VISTA: computational tools for comparative genomics.

Nucleic acids research ·Vol. 32 ·No. Web Server issue ·2004-07-01 ·Pages W273-9

Frazer KA, Pachter L, Poliakov A, Rubin EM, Dubchak I

Abstract

Comparison of DNA sequences from different species is a fundamental method for identifying functional elements in genomes. Here, we describe the VISTA family of tools created to assist biologists in carrying out this task. Our first VISTA server at http://www-gsd.lbl.gov/vista/ was launched in the summer of 2000 and was designed to align long genomic sequences and visualize these alignments with associated functional annotations. Currently the VISTA site includes multiple comparative genomics tools and provides users with rich capabilities to browse pre-computed whole-genome alignments of large vertebrate genomes and other groups of organisms with VISTA Browser, to submit their own sequences of interest to several VISTA servers for various types of comparative analysis and to obtain detailed comparative analysis results for a set of cardiovascular genes. We illustrate capabilities of the VISTA site by the analysis of a 180 kb interval on human chromosome 5 that encodes for the kinesin family member 3A (KIF3A) protein.

MeSH Terms
Binding Sites Chromosomes, Human, Pair 5 Computational Biology Genome, Human Genomics Humans Internet Kinesins/genetics Phylogeny Regulatory Sequences, Nucleic Acid Sequence Alignment Sequence Analysis, DNA Software Transcription Factors/metabolism
Chemicals
KIF3A protein, human Transcription Factors Kinesins
Authors & Affiliations
5 authors, click to expand affiliations / ORCID
Frazer Kelly A
Perlegen Sciences, Inc., 2021 Stierlin Court, Mountain View, CA 94043, USA.
Pachter Lior
Poliakov Alexander
Rubin Edward M
Dubchak Inna
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Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/gkh458
Published
2004-07-01
Pages
W273-9
Language
English
Region
England
NLM ID
0411011
PMCID
PMC441596
Subset
IM
External Links
PubMed source DOI: 10.1093/nar/gkh458 PMC Full Text View journal details
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