National Center for Genome Resources Provides 'MAR-Finder,' a Gene Sequence Analysis Tool

A new computer-based gene sequence analysis tool used to identify DNA regions involved in attachment to the nuclear matrix has been created by a researcher with the National Center for Genome Resources. The tool, called MAR-Finder, is available through the center's Web site at [NCGR URL not available; see http://www.futuresoft.org/MAR-Wiz/].

MAR-Finder is among several new Web-based tools developed by the scientific staff at the center to analyze gene sequences or to improve access to the sequences and valuable annotation in NCGR's Genome Sequence DataBase. Scientists in academia and private industry use the database and bioinformatics services provided by NCGR to conduct leading-edge research in genetics, medicine and functional genomics.

MAR-Finder, developed by senior computational scientist Gautam B. Singh, uses statistical inference to deduce the presence of matrix association regions, or MARs, in DNA sequences. MARs constitute a significant functional block within sequences and facilitate differential gene expression and DNA replication. MAR-Finder is ideal for researchers interested in DNA structure and identification of genes within a sequence.

The tool already has been used to discover a new human gene, called SOCS-1. Stephen A. Krawetz, associate professor of Ob/Gyn with the Center for Molecular Medicine & Genetics at Wayne State University in Detroit and collaborator with Singh on the development of MAR-Finder, used the tool to confirm the presence of a gene that other sequence analysis methods had failed to detect. With the tool he found the matrix association region and then identified the new gene, 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 said. "And appreciation for the role of MARs in controlling the expression of our genome is growing."

Other new tools available through NCGR include the Ad Hoc Query Tool, which allows users to query GSDB using Structured Query Language (SQL), and Excerpt, which extracts a selected span or spans from any public sequence in GSDB. An enhanced MAR-Finder with even more power is due out in mid-1998.

The National Center for Genome Resources is a non-profit bioinformatics organization based in Santa Fe, N.M., serving science and society.