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SFmap specifications


Unique identifier OMICS_09624
Name SFmap
Interface Web user interface
Restrictions to use None
Input data A Human genomic sequence or a list of sequences in FASTA format
Output data SFmap results are provided both as a text file and as a graphical web interface.
Computer skills Basic
Version 1.8
Stability Stable
Maintained Yes


  • person_outline Inbal Paz <>

Publications for SFmap

SFmap citations


Haplotype specific MAPT exon 3 expression regulated by common intronic polymorphisms associated with Parkinsonian disorders

PMCID: 5663040
PMID: 29084565
DOI: 10.1186/s13024-017-0224-6

[…] boundaries are those most often associated with an alternative splicing phenotype []. we therefore analysed 2 variants (rs1800547 and rs17651213) that fall within 100 bp downstream of exon 3 using sfmap, spliceaid2 and esefinder to predict the binding sites of common splice factors [–]. we identified putative splice factor binding sites at the rs1800547 and rs17651213 snp sequences […]


Both Maintenance and Avoidance of RNA Binding Protein Interactions Constrain Coding Sequence Evolution

PMCID: 5400389
PMID: 28138077
DOI: 10.1093/molbev/msx061

[…] were identical, except that pssms originating from rnacompete were ignored for mouse (this was to avoid including a large set of pssms determined originally for human in the mouse analysis)., sfmap consensuses were obtained from sfmap.technion.ac.il/sf_list.html (; last accessed 12 november 2015) and added to the list of motifs. sfmap does not distinguish between human and mouse […]


Comprehensive identification of internal structure and alternative splicing events in circular RNAs

PMCID: 4931246
PMID: 27350239
DOI: 10.1038/ncomms12060

[…] sites for 21 human splicing factors and 95 rna-binding proteins were then predicted for each exon and its adjacent intronic/intergenic sequences with two folds of exon lengths using online tools sfmap and rbpmap, respectively. the binding density was then calculated as the percentage of binding sites in the whole length of the sequence for prediction. for each subset of exons, such binding […]


Mutational analysis of SCN5A gene in long QT syndrome

PMCID: 4561237
PMID: 26401487
DOI: 10.1016/j.mgene.2015.07.010

[…] disequilibrium was inferred by haploview software ()., the splice binding sites were predicted by rainbow splicing: ebi databases asd alternative splicing (www.ebi.ac.uk/asd-srv/wb.cgi) and http://sfmap.technion.ac.il/ (). secondary mrna structure predictions were carried out by genebee online tool genebee.msu.su/services/rna2_reduced.html and http://rna.tbi.univie.ac.at/cgi-bin/rnafold.cgi […]


Muscleblind Like 1 and Muscleblind Like 3 Depletion Synergistically Enhances Myotonia by Altering Clc 1 RNA Translation

PMCID: 4588380
PMID: 26501102
DOI: 10.1016/j.ebiom.2015.07.028

[…] cytoplasmic and membrane fractions from wild type and mbnl1δe3/δe3/mbnl3δe2 mice (fig. s12)., we analyzed clc-1 mrna sequences to identify the putative mbnl1 and mbnl3 binding sites by using sfmap (). we identified 21 and 34 binding sites in the coding region, whereas only 2 and 3 binding sites were found in 3′ utr for mbnl1 and mbnl3, respectively (fig. s3a). we then determined whether […]


Cosplicing network analysis of mammalian brain RNA Seq data utilizing WGCNA and Mantel correlations

PMCID: 4429622
PMID: 26029240
DOI: 10.3389/fgene.2015.00174

[…] meaning that the number of tfbs in the intersection was at least half of all the tfbs detected in the two genes., computationally predicted splicing factor binding sites were acquired from the sfmap database (akerman et al., ; paz et al., ). first, we retrieved from biomart the genomic coordinates of all genes in our networks. the genomic coordinates were used as input to the sfmap […]

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SFmap institution(s)
Department of Biology, the Technion - Israel Institute of Technology, Haifa, Israel; Department of Computer Science, Technion - Israel Institute of Technology, Haifa, Israel

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