Inna Dubchak and Dmitriy V Ryaboy Summary

Comparative analysis of DNA sequences is becoming one of the major methods for discovery of functionally important genomic intervals. Presented here the VISTA family of computational tools was built to help researchers in this undertaking. These tools allow the researcher to align DNA sequences, quickly visualize conservation levels between them, identify highly conserved regions, and analyze sequences of interest through one of the following approaches:

• Browse precomputed whole-genome alignments of vertebrates and other groups of organisms.

• Submit sequences to GenomeVISTA to align them to whole genomes.

• Submit two or more sequences to mVISTA to align them with each other (a variety of alignment programs with several distinct capabilities are made available).

• Submit sequences to Regulatory VISTA (rVISTA) to perform transcription factor binding site predictions based on conservation within sequence alignments.

• Use stand-alone alignment and visualization programs to run comparative sequence analysis locally.

All VISTA tools use standard algorithms for visualization and conservation analysis to make comparison of results from different programs more straightforward. The web page serves as a portal for access to all VISTA tools. Our support group can be reached by email at [email protected].

Key Words: VISTA; comparative genomics; global DNA alignment; visualization; genome browser; sequence analysis.

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