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Comparative Analysis and Visualization of Genomic Sequences Using VISTA Browser and Associated Computational Tools

  • Inna Dubchak
Part of the Methods in Molecular Biology™ book series (MIMB, volume 395)

Summary

This chapter discusses VISTA Browser and associated computational tools for analysis and visual exploration of genomic alignments. The availability of massive amounts of genomic data produced by sequencing centers stimulated active development of computational tools for analyzing sequences and complete genomes, including tools for comparative analysis. Among algorithmic and computational challenges of such analysis, i.e., efficient and fast alignment, decoding of evolutionary history, the search for functional elements in genomes, and others, visualization of comparative results is of great importance. Only interactive viewing and manipulation of data allow for its in-depth investigation by biologists.

We describe the rich capabilities of the interactive VISTA Browser with its extensions and modifications, and provide examples of the examination of alignments of DNA sequences and whole genomes, both eukaryotic and microbial. VISTA portal (http://genome.lbl.gov/vista) provides access to all these tools.

Keywords

Comparative genomics alignment visualization genome browser VISTA 

Notes

Acknowledgments

The author is grateful to Michael Cipriano and Alexander Levin for their help with the manuscript. The VISTA project is an ongoing collaborative effort of a large group of scientists and engineers. It has been developed and maintained in the Genomics Division of Lawrence Berkeley National Laboratory. The names of all contributors are found at the VISTA website (http://genome.lbl.gov/vista).

The project was partially supported by the grant no. HL88728, Berkeley-PGA, under the Programs for Genomic Application, funded by the US National Heart, Lung, and Blood Institute, and performed under Department of Energy Contract DE-AC0378SF00098, University of California.

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Copyright information

© Humana Press Inc. 2007

Authors and Affiliations

  • Inna Dubchak
    • 1
  1. 1.Lawrence Berkeley National LaboratoryBerkeley

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