Sponsored by the U.S. Department of Energy Human Genome Program
Human Genome News Archive Edition
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VISTA Software Widens Comparative View
With the increasing availability of human and mouse genomic sequence, a challenge confronting biologists is how to convert these large amounts of data into useful biology. One of the more powerful algorithms for identifying functional regions in genomic DNA, including both genes and surrounding regulatory elements, involves comparative sequence analysis.
Confronted by a scarcity of tools for such studies, investigators led by Inna Dubchak and Edward Rubin in the Genome Sciences Department at Lawrence Berkeley National Laboratory (LBNL) have developed a suite of software tools called VISTA (VISualization Tools for Alignment). Incorporating a novel global- alignment procedure and components for visualization and analysis, VISTA enables large-scale comparisons between DNA sequences of two or more species. Its visual output is clean and simple, allowing for easy identification of conserved regions. Similarity scores are displayed for the entire sequence, thus helping in identification of shorter conserved regions or regions with gaps.
Various modifications of VISTA deal with particular biological problems. cVISTA (complementary VISTA) is used to look at differences between such recently evolved species as mice and rats or humans and chimpanzees. rVISTA (regulatory VISTA) combines a search of the transcription-factor binding-sites database with comparative sequence analysis, thus greatly reducing the number of predicted binding sites and suggesting plausible hypotheses for further biological studies. Used extensively in LBNL's Genome Sciences Department, VISTA also has become the main comparative sequence analysis tool of several large sequencing centers.
Individuals can use VISTA by anonymously sending sequence data to the Web site (www-gsd.lbl.gov/vista) or requesting a stand-alone computer program (free for academic institutions; modest licensing fee for private industry). More than 250 investigators have used VISTA online since it became available in July 2000, and close to 150 copies of the program have been distributed in academic institutions of 20 countries. [Edward Rubin, LBNL]
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The Human Genome Project (HGP) was an international 13-year effort, 1990 to 2003. Primary goals were to discover the complete set of human genes and make them accessible for further biological study, and determine the complete sequence of DNA bases in the human genome. See Timeline for more HGP history.
Published from 1989 until 2002, this newsletter facilitated HGP communication, helped prevent duplication of research effort, and informed persons interested in genome research.