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VISTA: computational tools for comparative genomics

Kelly A. FrazerPerlegen Sciences, Inc., 2021 Stierlin Court, Mountain View, CA 94043, USALior PachterDepartment of Mathematics, University of California-Berkeley, Berkeley, CA, 94720, USA,Alexandre PoliakovGenomics Division, Lawrence Berkeley National Laboratory, MS 84-171, Berkeley, CA 94720, USA andEdward M. RubinDepartment of Energy Joint Genome Institute, 2800 Mitchell Avenue, Walnut Creek, CA 94598, USAInna DubchakDepartment of Energy Joint Genome Institute, 2800 Mitchell Avenue, Walnut Creek, CA 94598, USA

2004en

ABI

Annotatsiya

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.

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Identifikatorlar

DOI: 10.1093/nar/gkh458

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