VISTA: computational tools for comparative genomics

TLDR

Comparison of DNA sequences from different species is a fundamental method for identifying functional elements in genomes. The authors present the VISTA family of tools to help biologists perform comparative genomics analyses. The VISTA platform, launched in 2000, offers servers that align long genomic sequences, visualize alignments with functional annotations, provide pre‑computed whole‑genome alignments for large vertebrate genomes, allow users to submit custom sequences for diverse comparative analyses, and deliver detailed results, as demonstrated by a 180 kb analysis of the human KIF3A locus.

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.