STAMP

A web tool for exploring DNA-binding motif similarities

Shaun A. Mahony, Panayiotis V. Benos

Research output: Contribution to journalArticle

302 Citations (Scopus)

Abstract

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.

Original languageEnglish (US)
JournalNucleic acids research
Volume35
Issue numberSUPPL.2
DOIs
StatePublished - Jul 1 2007

Fingerprint

Nucleotide Motifs
Databases
Sequence Alignment
Consensus Sequence
Transcription Factors
Software
Binding Sites
Datasets

All Science Journal Classification (ASJC) codes

  • Genetics

Cite this

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STAMP : A web tool for exploring DNA-binding motif similarities. / Mahony, Shaun A.; Benos, Panayiotis V.

In: Nucleic acids research, Vol. 35, No. SUPPL.2, 01.07.2007.

Research output: Contribution to journalArticle

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