title: VISTA: computational tools for comparative genomics.
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.
authors.affiliation: Perlegen Sciences, Inc., 2021 Stierlin Court, Mountain View, CA 94043, USA.
authors.forename: Kelly A
authors.initials: KA
authors.lastname: Frazer
authors.forename: Lior
authors.initials: L
authors.lastname: Pachter
authors.forename: Alexander
authors.initials: A
authors.lastname: Poliakov
authors.forename: Edward M
authors.initials: EM
authors.lastname: Rubin
authors.forename: Inna
authors.initials: I
authors.lastname: Dubchak
mesh_terms: D001665:Binding Sites; D002895:Chromosomes, Human, Pair 5; D019295:Computational Biology; D015894:Genome, Human; D023281:Genomics; D006801:Humans; D020407:Internet; D016547:Kinesins / Q000235:genetics; D010802:Phylogeny; D012045:Regulatory Sequences, Nucleic Acid; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D012984:Software; D014157:Transcription Factors / Q000378:metabolism
chemical_list: C087415:KIF3A protein, human; D014157:Transcription Factors; D016547:Kinesins