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Faced With a Better Mouse Assembly, Scientist Tweaks a Bioinformatics Stalwart

SAN FRANCISCO, March 28 - While some researchers build a better mouse assembly, others have their eyes on creating the perfect tool to use it. Inna Dubchak, a staff scientist at the National Energy Research Scientific Computing Center at Lawrence Berkeley National Laboratory here, is one of these scientists.

Anticipating the release of an updated mouse genome by the International Mouse Sequence Consortium in the next few weeks, Dubchak has been upgrading the suite of bioinformatics tools she created two years ago to help staff biologists compare and visualize various genomes.


The tools, called VISTA, or visualization tools for alignment, analyze long sequence alignments of DNA from two or more species and put the results in graphic form. Scientists at Berkeley, including those from the lab's genome-sciences department who worked with Dubchak to create the software, use it to hunt for functional elements in the human genome.


The use of VISTA has been steadily increasing since its debut in July 2000, when six people submitted online a pair of sequences from multiple organisms for comparison and analysis. One year later that number grew to 418, and in February 2002 there were 886 requests.


Dubchak says that reliance on VISTA, accessible at, will increase significantly with the greater coverage emerging for the mouse genome and the burgeoning list of new species being sequenced.


"More genome sequences are becoming available, not just for the mouse but other organisms," Dubchak told GenomeWeb in a recent interview. "People are becoming much more interested in comparative genomics now than a year ago because a lot of important discoveries were made [recently] using comparative genomics, such as discovering new genes and other functional elements


"Comparative genomics has attracted a lot of attention in the last year or so," she added.

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