Nucleic Acids Research, 1995, Vol. 23, No. 23 4878-4884
© 1995
Articles |
Matlnd and Matlnspector: new fast and versatile tools for detection of consensus matches in nucleotide sequence data
1Institut für Säugetiergenetik, GSF-Forschungszentrum für Umwelt und Gesundheit GmbH Ingolstädter Landstraße 1, D-85758 Neuherberg, Germany 2Abteilung Genetik, Gesellschaft für Biotechnologische Forschung mbH Mascheroder Weg 1, D-38124 Braunschweig, Germany
*To whom correspondence should be addressed
Received August 11, 1995. Accepted October 26, 1995.
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.
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Z. Jiang, Z. Wang, T. Kunej, G. A. Williams, J. J. Michal, X.-L. Wu, and N. S. Magnuson A Novel Type of Sequence Variation: Multiple-Nucleotide Length Polymorphisms Discovered in the Bovine Genome Genetics, May 1, 2007; 176(1): 403 - 407. [Abstract] [Full Text] [PDF]
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S. Argimon, J. A. Wishart, R. Leng, S. Macaskill, A. Mavor, T. Alexandris, S. Nicholls, A. W. Knight, B. Enjalbert, R. Walmsley, et al. Developmental Regulation of an Adhesin Gene during Cellular Morphogenesis in the Fungal Pathogen Candida albicans Eukaryot. Cell, April 1, 2007; 6(4): 682 - 692. [Abstract] [Full Text] [PDF]
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A. Buchberger, D. Freitag, and H.-H. Arnold A homeo-paired domain-binding motif directs Myf5 expression in progenitor cells of limb muscle Development, March 15, 2007; 134(6): 1171 - 1180. [Abstract] [Full Text] [PDF]
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 R.-A. Cue, S. I. Nicolau-Solano, J. D. McGivan, J. D. Wood, and O. Doran Breed-associated variations in the sequence of the pig 3{beta}-hydroxysteroid dehydrogenase gene J Anim Sci, March 1, 2007; 85(3): 571 - 576. [Abstract] [Full Text] [PDF]
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M.-H. Hsu, U. Savas, K. J. Griffin, and E. F. Johnson Regulation of Human Cytochrome P450 4F2 Expression by Sterol Regulatory Element-binding Protein and Lovastatin J. Biol. Chem., February 23, 2007; 282(8): 5225 - 5236. [Abstract] [Full Text] [PDF]
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C. Galuschka, M. Schindler, L. Bulow, and R. Hehl AthaMap web tools for the analysis and identification of co-regulated genes Nucleic Acids Res., January 12, 2007; 35(suppl_1): D857 - D862. [Abstract] [Full Text] [PDF]
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A. G. Jegga, J. Chen, S. Gowrisankar, M. A. Deshmukh, R. Gudivada, S. Kong, V. Kaimal, and B. J. Aronow GenomeTrafac: a whole genome resource for the detection of transcription factor binding site clusters associated with conventional and microRNA encoding genes conserved between mouse and human gene orthologs Nucleic Acids Res., January 12, 2007; 35(suppl_1): D116 - D121. [Abstract] [Full Text] [PDF]
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N. J. Butcher, N. L. Tetlow, C. Cheung, G. M. Broadhurst, and R. F. Minchin Induction of Human Arylamine N-Acetyltransferase Type I by Androgens in Human Prostate Cancer Cells Cancer Res., January 1, 2007; 67(1): 85 - 92. [Abstract] [Full Text] [PDF]
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M. Corton, J. I. Botella-Carretero, A. Benguria, G. Villuendas, A. Zaballos, J. L. San Millan, H. F. Escobar-Morreale, and B. Peral Differential Gene Expression Profile in Omental Adipose Tissue in Women with Polycystic Ovary Syndrome J. Clin. Endocrinol. Metab., January 1, 2007; 92(1): 328 - 337. [Abstract] [Full Text] [PDF]
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X. Li, E. Calvo, M. Cool, P. Chrobak, D. G. Kay, and P. Jolicoeur Overexpression of Notch1 Ectodomain in Myeloid Cells Induces Vascular Malformations through a Paracrine Pathway Am. J. Pathol., January 1, 2007; 170(1): 399 - 415. [Abstract] [Full Text] [PDF]
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