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

Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder 80309-0347, USA.
Computer applications in the biosciences: CABIOS 11/1995; 11(5):563-6. DOI: 10.1093/bioinformatics/11.5.563
Source: PubMed

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.

  • [Show abstract] [Hide abstract]
    ABSTRACT: A variety of patterns have been observed on the DNA and protein sequences that serve as control points for gene expression and cellular functions. Owing to the vital role of such patterns discovered on biological sequences, they are generally cataloged and maintained within internationally shared databases. Furthermore,the variability in a family of observed patterns is often represented using computational models in order to facilitate their search within an uncharacterized biological sequence. As the biological data is comprised of a mosaic of sequence-levels motifs, it is significant to unravel the synergies of macromolecular coordination utilized in cell-specific differential synthesis of proteins. This article provides an overview of the various pattern representation methodologies and the surveys the pattern databases available for use to the molecular biologists. Our aim is to describe the principles behind the computational modeling and analysis techniques utilized in bioinformatics research, with the objective of providing insight necessary to better understand and effectively utilize the available databases and analysis tools. We also provide a detailed review of DNA sequence level patterns responsible for structural conformations within the Scaffold or Matrix Attachment Regions (S/MARs).
    Molecular Biotechnology 03/2005; 29(2):165-83. · 2.26 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: Gene expression in higher organisms, is, to a large degree, controlled at the level of transcription, where DNA-binding proteins (transcription factors) play an influential role in gene regulation. This is achieved through various mechanisms, including those that involve silencer and enhancer regions. Variation in those regulatory regions, as well as in the genes encoding the transcription factors, has been shown to generate functional effects at the molecular, cellular, and neurobehavioral levels. The aim of the present paper is two-fold. First, for the sake of clarity and to reintroduce the terminology to Behavior Genetics readers, we review the concepts of gene structure, gene expression, and gene regulation. Second, using distinct bioinformatic tools, we set out to identify transcription factors that could be involved in the transcriptional regulation of genes known to be associated with aggressive behavior in mice. The results of this in silico study reveal common putative transcription factor binding sites among the set of genes investigated (especially for SRY), suggesting similar molecular transcriptional mechanisms.
    Behavior Genetics 10/2003; 33(5):549-62. · 2.61 Impact Factor
  • Source
    Bioinformatics. 01/1999; 15:180-186.

Full-text (2 Sources)

Available from
May 21, 2014