VISTA: computational tools for comparative genomics - PubMed (original) (raw)

. 2004 Jul 1;32(Web Server issue):W273-9.

doi: 10.1093/nar/gkh458.

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VISTA: computational tools for comparative genomics

Kelly A Frazer et al. Nucleic Acids Res. 2004.

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.

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Figures

Figure 1

Figure 1

(a) VISTA Browser (VGB2.0) plot of the 180 kb interval (chr5:131949456–132139102 on the NCBI build 34 human assembly) containing KIF3A, accessible through the gateway at

http://www-gsd.lbl.gov/vista

or

http://pipeline.lbl.gov

. Visualization plots show conserved sequences between humans and mice (top panel) and humans and rats (bottom panel) based on the multiple three-genome alignment using MLAGAN. The level of conservation (vertical axis) is displayed in the coordinates of the human sequence (horizontal axis). Conserved regions above the level of 70%/100 bp are highlighted under the curve, with red indicating a conserved non-coding region, blue, a conserved exon, and turquoise, an untranslated region. Details of the display are given in the legend on the left-hand side of the plot. The ‘UCSC’ button opens another window containing the mirrored UCSC browser view of the same interval with integrated VISTA tracks. The browser is provided with extensive on-line help. (b) VISTA Browser generated list of conserved human/mouse elements in the KIF3A region with their coordinates in the human (unbracketed numbers) and mouse (bracketed numbers) sequence, lengths and percentage identities, and functional annotation. Elements from the beginning of the 180 kb interval in RAD50 are shown. (c) Genomic fragment upstream of KIF3A gene containing multiple conserved non-coding elements. The number of conserved elements (colored) depends on the user-selected percentage identity and length cutoffs shown above each plot.

Figure 2

Figure 2

VISTA Browser plot generated by the submission of the draft dog genomic sequence (GenBank accession number AF276990) to the GenomeVISTA server. The dog sequence is automatically aligned against the orthologous human region. The bar at the bottom of the plot shows the locations of draft fragments in the aligned sequence; gray indicates that the sequence is present and white indicates that it is missing.

Figure 3

Figure 3

rVISTA visualization of predicted binding sites for the AP2REP and ZIC2 transcription factors in the interval downstream of KIF3A. Only the predicted binding sites that are evolutionarily conserved are displayed.

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