Cited by 102RNA Research and SplicingGenomics and Phylogenetic StudiesGenomics and Chromatin Dynamics

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

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Paz, I., Akerman, M., Dror, I., Kosti, I., Mandel-Gutfreund, Y.·2010·Nucleic Acids Research

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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.

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Figure 1. SFmap output shown in a ‘dense’ (A) and a ‘full’ (B) format. In this example, SFmap was run on the 3′-UTR of the SC35 gene. The predicted sites for the motifs selected by the user are displayed on the UCSC HG Browser as a custom track. The top five motifs were selected from motifs that were stored in our database, and the last motif is a user-defined motif. As can be observed, most of the predicted binding sites of the three SFs are mapped to the intron/exon junction previously shown to be regulated by these factors (18).CC BY-NC · PubMed Central

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Une nouvelle fonction pour la DEAD-box ARN hélicase p68/DDX5 dans la Dystrophie Myotonique de type 1
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Authors: Paz, I., Akerman, M., Dror, I., Kosti, I., & Mandel-Gutfreund, Y.
Affiliations: Technion – Israel Institute of Technology (IL)
ORCID: Paz, I.
Akerman, M.
Dror, I.
Kosti, I.
Venue: Nucleic Acids Research
Publisher: Oxford University Press (OUP)
Published: 2010-05-25
Volume: 38
Issue: Web Server
Pages: W281-W285
ISSN: 0305-1048 (ISSN-L)
1362-4962
DOI: 10.1093/nar/gkq444
PMC: PMC2896136
OpenAlex: W1988971922
Cited by: 102
References: 22
Citations by year: 2025: 2 · 2023: 4 · 2022: 6 · 2021: 4 · 2020: 3 · 2019: 9 · 2018: 5 · 2017: 9 · 2016: 10 · 2015: 11 · 2014: 16 · 2013: 6 · 2012: 9
FWCI: 2.73
Type: journal article
Language: en
Open access: gold
doi.org
Licence: cc-by-nc
creativecommons.org/licenses/by-nc/2.5 (vor, 2324 d)
Locations: Nucleic Acids Research (publishedVersion, cc-by-nc)
PubMed Central (publishedVersion, cc-by-nc)
PubMed (publishedVersion)
Cold Spring Harbor Laboratory Institutional Repository (Cold Spring Harbor Laboratory) (acceptedVersion)
HighWire Press Open Archive (submittedVersion)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
Keywords: alternative splicing, evolutionary conservation, human genome sequence, web server
MeSH terms: Algorithms, Binding Sites, Humans, Software, User-Computer Interface, Genome, Human, RNA-Binding Proteins, Alternative Splicing, Sequence Analysis, RNA, Internet

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

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