STAMP: a web tool for exploring DNA-binding motif similarities

By Shaun Mahony, Panayiotis V. Benos. Nucleic Acids Res., 2007

509 citations recorded by the source corpus.

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

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/3bf959ca80818eb7fb5401fe70277d68e4910a5e

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Citations in the corpus

JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update (2007, methodology): “(27,28) made a comprehensive study on alignments of matrices and construction of familial binding proﬁles, resulting in the STAMP tool, which is now used within JASPAR to cluster matrix models.”
Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo (2010, unknown): “The TF-motif divergence bears similarity to earlier comparison strategies (Roepcke et al, 2005; Mahony and Benos, 2007) in the use of KL divergence but as far as we know, taking the minimum is a novel feature.”