SFmap: a web server for motif analysis and prediction of splicing factor binding sites

Paz, I., Akerman, M., Dror, I., Kosti, I., Mandel-Gutfreund, Y. (May 2010) SFmap: a web server for motif analysis and prediction of splicing factor binding sites. Nucleic Acids Research, 38 (S2). W281-W285. ISSN 03051048 (ISSN)

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URL: http://www.ncbi.nlm.nih.gov/pubmed/20501600
DOI: 10.1093/nar/gkq444

Abstract

Alternative splicing (AS) is a post-transcriptional process considered to be responsible for the huge diversity of proteins in higher eukaryotes. AS events are regulated by different splicing factors (SFs) that bind to sequence elements on the RNA. SFmap is a web server for predicting putative SF binding sites in genomic data (http://sfmap.technion.ac.il). SFmap implements the COS(WR) algorithm, which computes similarity scores for a given regulatory motif based on information derived from its sequence environment and its evolutionary conservation. Input for SFmap is a human genomic sequence or a list of sequences in FASTA format that can either be uploaded from a file or pasted into a window. SFmap searches within a given sequence for significant hits of binding motifs that are either stored in our database or defined by the user. SFmap results are provided both as a text file and as a graphical web interface.

Item Type: Paper
Subjects: bioinformatics > genomics and proteomics > computers > computer software
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification > protein expression > post-translational modification
CSHL Authors:
Communities: CSHL Post Doctoral Fellows
CSHL labs > Krainer lab
Depositing User: CSHL Librarian
Date: 25 May 2010
Date Deposited: 05 Oct 2011 13:55
Last Modified: 01 May 2013 16:46
PMCID: PMC2896136
Related URLs:
URI: http://repository.cshl.edu/id/eprint/15503

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