Nucleic Acids Research Advance Access originally published online on May 3, 2007
Nucleic Acids Research 2007 35(Web Server issue):W253-W258; doi:10.1093/nar/gkm272
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Nucleic Acids Research, 2007, Vol. 35, No. suppl_2 W253-W258
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
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STAMP: a web tool for exploring DNA-binding motif similarities
1Department of Computational Biology, School of Medicine, University of Pittsburgh and 2Department of Human Genetics, Graduate School of Public Health, and University of Pittsburgh Cancer Institute, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
*To whom correspondence should be addressed. Tel: +412 648 3315; Fax: +412 648 3163; Email: benos{at}pitt.edu or shaun.mahony{at}ccbb.pitt.edu
Received January 31, 2007. Accepted April 10, 2007.
STAMP is a newly developed web server that is designed to support the study of DNA-binding motifs. STAMP may be used to query motifs against databases of known motifs; the software aligns input motifs against the chosen database (or alternatively against a user-provided dataset), and lists of the highest-scoring matches are returned. Such similarity-search functionality is expected to facilitate the identification of transcription factors that potentially interact with newly discovered motifs. STAMP also automatically builds multiple alignments, familial binding profiles and similarity trees when more than one motif is inputted. These functions are expected to enable evolutionary studies on sets of related motifs and fixed-order regulatory modules, as well as illustrating similarities and redundancies within the input motif collection. STAMP is a highly flexible alignment platform, allowing users to ‘mix-and-match’ between various implemented comparison metrics, alignment methods (local or global, gapped or ungapped), multiple alignment strategies and tree-building methods. Motifs may be inputted as frequency matrices (in many of the commonly used formats), consensus sequences, or alignments of known binding sites. STAMP also directly accepts the output files from 12 supported motif-finders, enabling quick interpretation of motif-discovery analyses. STAMP is available at http://www.benoslab.pitt.edu/stamp
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