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Nucleic Acids Res. 2010 Jul;38(Web Server issue):W281-5. doi: 10.1093/nar/gkq444. Epub 2010 May 25.

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

Author information

1
Faculty of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel.

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.

PMID:
20501600
PMCID:
PMC2896136
DOI:
10.1093/nar/gkq444
[Indexed for MEDLINE]
Free PMC Article

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