MATRIX SEARCH 1.0: A computer program that scans DNA sequences for transcriptional elements using a database of weight matrices

Qing K. Chen; Gerald Z. Hertz; Gary D. Stormo

doi:10.1093/bioinformatics/11.5.563

MATRIX SEARCH 1.0: A computer program that scans DNA sequences for transcriptional elements using a database of weight matrices

Qing K. Chen, Gerald Z. Hertz, Gary D. Stormo

Research output: Contribution to journal › Article › peer-review

114 Scopus citations

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.

Original language	English
Pages (from-to)	563-566
Number of pages	4
Journal	Bioinformatics
Volume	11
Issue number	5
DOIs	https://doi.org/10.1093/bioinformatics/11.5.563
State	Published - Oct 1995

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title = "MATRIX SEARCH 1.0: A computer program that scans DNA sequences for transcriptional elements using a database of weight matrices",

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.",

author = "Chen, {Qing K.} and Hertz, {Gerald Z.} and Stormo, {Gary D.}",

note = "Funding Information: We would like to thank Dr Dan Prestndge of University of Minnesota for his suggestions, and source code for the user interface. We would also like to thank Dr David Ghosh for suggestions and database, and Dr Edgar Wingender for database. This research is supported by NIH grants 7F32HG00124 and NIH HG00249.",

year = "1995",

month = oct,

doi = "10.1093/bioinformatics/11.5.563",

language = "English",

volume = "11",

pages = "563--566",

journal = "Bioinformatics",

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T2 - A computer program that scans DNA sequences for transcriptional elements using a database of weight matrices

AU - Chen, Qing K.

AU - Hertz, Gerald Z.

AU - Stormo, Gary D.

N1 - Funding Information: We would like to thank Dr Dan Prestndge of University of Minnesota for his suggestions, and source code for the user interface. We would also like to thank Dr David Ghosh for suggestions and database, and Dr Edgar Wingender for database. This research is supported by NIH grants 7F32HG00124 and NIH HG00249.

PY - 1995/10

Y1 - 1995/10

N2 - 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.

AB - 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.

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MATRIX SEARCH 1.0: A computer program that scans DNA sequences for transcriptional elements using a database of weight matrices

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