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New Sequence Analysis Tool, Available on Web, Has Discovered a Gene

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SANTA FE, NM--The National Center for Genome Resources, a nonprofit bioinformatics organization here, has released MAR-Finder, a new computer-based gene sequence analysis tool, on its web site at http://www.ncgr.org/MarFinder/. MAR-Finder can be used to identify DNA regions involved in attachment to the nuclear matrix, according to the center.

MAR-Finder was developed by senior computational scientist Gautam Singh. It uses statistical inference to deduce the presence of matrix association regions, or MAR's, in DNA sequences. MAR's constitute a significant functional block within sequences and facilitate differential gene expression and DNA replication, he said. The tool has already been used by Stephen Krawetz, an associate professor at the Center for Molecular Medicine and Genetics at Wayne State University and collaborator with Singh, to discover a new human gene, known as SOCS-1, which is involved in human cytokine-mediated signal transduction.

"MAR-Finder is a valuable tool and its development was a nice meld between a dry and wet lab. You can detect a matrix association region with the computer and test your prediction at the bench that same day," Krawetz commented. "And, appreciation for the role of MARs in controlling the expression of our genome is growing." An enhanced version of MAR-Finder with even more power is due out in the middle of the year.

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