T-Reg Comparator: an analysis tool for the comparison of position weight matrices

Röpcke S, Grossmann S, Rahmann S, Vingron M (2005)
Nucleic Acids Research 33(Web Server): W438-W441.

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Zeitschriftenaufsatz | Veröffentlicht | Englisch
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Abstract / Bemerkung
T-Reg Comparator is a novel software tool designed to support research into transcriptional regulation. Sequence motifs representing transcription factor binding sites are usually encoded as position weight matrices. The user inputs a set of such weight matrices or binding site sequences and our program matches them against the T-Reg database, which is presently built on data from the Transfac [E. Wingender (2004) In Silico Biol., 4, 55-61] and Jaspar [A. Sandelin, W. Alkema, P. Engstrom, W. W. Wasserman and B. Lenhard (2004) Nucleic Acids Res., 32, D91-D94]. Our tool delivers a detailed report on similarities between user-supplied motifs and motifs in the database. Apart from simple one-to-one relationships, T-Reg Comparator is also able to detect similarities between submatrices. In addition, we provide a user interface to a program for sequence scanning with weight matrices. Typical areas of application for T-Reg Comparator are motif and regulatory module finding and annotation of regulatory genomic regions. T-Reg Comparator is available at http://treg.molgen.mpg.de.
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Zeitschriftentitel
Nucleic Acids Research
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33
Zeitschriftennummer
Web Server
Seite
W438-W441
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Röpcke S, Grossmann S, Rahmann S, Vingron M. T-Reg Comparator: an analysis tool for the comparison of position weight matrices. Nucleic Acids Research. 2005;33(Web Server):W438-W441.
Röpcke, S., Grossmann, S., Rahmann, S., & Vingron, M. (2005). T-Reg Comparator: an analysis tool for the comparison of position weight matrices. Nucleic Acids Research, 33(Web Server), W438-W441. doi:10.1093/nar/gki590
Röpcke, S., Grossmann, S., Rahmann, S., and Vingron, M. (2005). T-Reg Comparator: an analysis tool for the comparison of position weight matrices. Nucleic Acids Research 33, W438-W441.
Röpcke, S., et al., 2005. T-Reg Comparator: an analysis tool for the comparison of position weight matrices. Nucleic Acids Research, 33(Web Server), p W438-W441.
S. Röpcke, et al., “T-Reg Comparator: an analysis tool for the comparison of position weight matrices”, Nucleic Acids Research, vol. 33, 2005, pp. W438-W441.
Röpcke, S., Grossmann, S., Rahmann, S., Vingron, M.: T-Reg Comparator: an analysis tool for the comparison of position weight matrices. Nucleic Acids Research. 33, W438-W441 (2005).
Röpcke, Stefan, Grossmann, Steffen, Rahmann, Sven, and Vingron, Martin. “T-Reg Comparator: an analysis tool for the comparison of position weight matrices”. Nucleic Acids Research 33.Web Server (2005): W438-W441.
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29 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

CoMoDis: composite motif discovery in mammalian genomes.
Donaldson IJ, Göttgens B., Nucleic Acids Res 35(1), 2007
PMID: 17130158
A new generation of JASPAR, the open-access repository for transcription factor binding site profiles.
Vlieghe D, Sandelin A, De Bleser PJ, Vleminckx K, Wasserman WW, van Roy F, Lenhard B., Nucleic Acids Res 34(database issue), 2006
PMID: 16381983
POXO: a web-enabled tool series to discover transcription factor binding sites.
Kankainen M, Pehkonen P, Rosenstöm P, Törönen P, Wong G, Holm L., Nucleic Acids Res 34(web server issue), 2006
PMID: 16845065

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