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MATRIX SEARCH 1.0: a computer program that scans DNA sequences for transcriptional elements using a database of
Q K Chen1, G Z Hertz, G D Stormo
1Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder 80309-0347, USA. chenq@boulder.colorado.edu
Abstract:
The information matrix database (IMD), a database of weight matrices of transcription factor binding sites, is developed. MATRIX SEARCH, a program which can find potential transcription factor binding sites in DNA sequences using the IMD database, is also developed and accompanies the IMD database. MATRIX SEARCH adopts a user interface very similar to that of the SIGNAL SCAN program. MATRIX SEARCH allows the user to search an input sequence with the IMD automatically, to visualize the matrix representations of sites for particular factors, and to retrieve journal citations. The source code for MATRIX SEARCH is in the 'C' language, and the program is available for unix platforms.