Matlnd and Matlnspector: new fast and versatile tools for detection of consensus matches in nucleotide sequence data

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ID: 290303
1995
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Abstract
The identification of potential regulatory motifs in new sequence data is increasingly important for experimental design. Those motifs are commonly located by matches to IUPAC strings derived from consensus sequences. Although this method is simple and widely used, a major drawback of IUPAC strings is that they necessarily remove much of the information originally present in the set of sequences. Nucleotide distribution matrices retain most of the information and are thus better suited to evaluate new potential sites. However, sufficiently large libraries of pre-compiled matrices are a prerequisite for practical application of any matrix-based approach and are just beginning to emerge. Here we present a set of tools for molecular biologists that allows generation of new matrices and detection of potential sequence matches by automatic searches with a library of pre-compiled matrices. We also supply a large library (>200) of transcription factor binding site matrices that has been compiled on the basis of published matrices as well as entries from the TRANSFAC database, with emphasis on sequences with experimentally verified binding capacity. Our search method includes position weighting of the matrices based on the information content of individual positions and calculates a relative matrix similarity. We show several examples suggesting that this matrix similarity is useful in estimating the functional potential of matrix matches and thus provides a valuable basis for designing appropriate experiments.
Reference Key
openalex_W2064879068 Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Kerstin Quandt, Kornelie Frech, Holger Karas, Edgar Wingender, Thomas Werner
Journal Nucleic Acids Research
Year 1995
DOI
10.1093/nar/23.23.4878
URL
https://doi.org/10.1093/nar/23.23.4878
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