Literature DB >> 8590181

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

Q K Chen1, G Z Hertz, G D Stormo.   

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.

Mesh：

Substances：

Year:  1995        PMID： 8590181     DOI： 10.1093/bioinformatics/11.5.563

Source DB:  PubMed          Journal:  Comput Appl Biosci        ISSN： 0266-7061


  32 in total

1.  SELEX_DB: an activated database on selected randomized DNA/RNA sequences addressed to genomic sequence annotation.

Authors:  J V Ponomarenko; G V Orlova; M P Ponomarenko; S V Lavryushev; A S Frolov; S V Zybova; N A Kolchanov
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

2.  ACTIVITY: a database on DNA/RNA sites activity adapted to apply sequence-activity relationships from one system to another.

Authors:  J V Ponomarenko; D P Furman; A S Frolov; N L Podkolodny; G V Orlova; M P Ponomarenko; N A Kolchanov; A Sarai
Journal:  Nucleic Acids Res       Date:  2001-01-01       Impact factor: 16.971

3.  In silico prediction of scaffold/matrix attachment regions in large genomic sequences.

Authors:  Matthias Frisch; Kornelie Frech; Andreas Klingenhoff; Kerstin Cartharius; Ines Liebich; Thomas Werner
Journal:  Genome Res       Date:  2002-02       Impact factor: 9.043

4.  The Krüppel-like factor 15 as a molecular link between myogenic factors and a chromosome 4q transcriptional enhancer implicated in facioscapulohumeral dystrophy.

Authors:  Petr Dmitriev; Andrei Petrov; Eugenie Ansseau; Luiza Stankevicins; Sébastien Charron; Elena Kim; Tomas Jan Bos; Thomas Robert; Ahmed Turki; Frédérique Coppée; Alexandra Belayew; Vladimir Lazar; Gilles Carnac; Dalila Laoudj; Marc Lipinski; Yegor S Vassetzky
Journal:  J Biol Chem       Date:  2011-09-21       Impact factor: 5.157

5.  MultiPipMaker and supporting tools: Alignments and analysis of multiple genomic DNA sequences.

Authors:  Scott Schwartz; Laura Elnitski; Mei Li; Matt Weirauch; Cathy Riemer; Arian Smit; Eric D Green; Ross C Hardison; Webb Miller
Journal:  Nucleic Acids Res       Date:  2003-07-01       Impact factor: 16.971

6.  MATCH: A tool for searching transcription factor binding sites in DNA sequences.

Authors:  A E Kel; E Gössling; I Reuter; E Cheremushkin; O V Kel-Margoulis; E Wingender
Journal:  Nucleic Acids Res       Date:  2003-07-01       Impact factor: 16.971

7.  Target Explorer: An automated tool for the identification of new target genes for a specified set of transcription factors.

Authors:  Alona Sosinsky; Christopher P Bonin; Richard S Mann; Barry Honig
Journal:  Nucleic Acids Res       Date:  2003-07-01       Impact factor: 16.971

8.  A non-parametric model for transcription factor binding sites.

Authors:  Oliver D King; Frederick P Roth
Journal:  Nucleic Acids Res       Date:  2003-10-01       Impact factor: 16.971

Review 9.  Databases, models, and algorithms for functional genomics: a bioinformatics perspective.

Authors:  Gautam B Singh; Harkirat Singh
Journal:  Mol Biotechnol       Date:  2005-02       Impact factor: 2.695

10.  Bayesian variable selection for gene expression modeling with regulatory motif binding sites in neuroinflammatory events.

Authors:  Kuang-Yu Liu; Xiaobo Zhou; Kinhong Kan; Stephen T C Wong
Journal:  Neuroinformatics       Date:  2006
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