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Protocols

HSF specifications

Information


Unique identifier OMICS_00176
Name HSF
Alternative name Human Splicing Finder
Interface Web user interface
Restrictions to use Academic or non-commercial use
Input data A single sequence
Computer skills Basic
Version 3.1
Stability Stable
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Maintainers


Publication for Human Splicing Finder

HSF citations

 (246)
call_split

Targeted next generation sequencing identifies functionally deleterious germline mutations in novel genes in early onset/familial prostate cancer

2018
PLoS Genet
PMCID: 5919682
PMID: 29659569
DOI: 10.1371/journal.pgen.1007355
call_split See protocol

[…] To explore the functional consequence of truncating/deleterious variants, MutationTaster [] and Uniprot [] were queried. To infer the putative impact on splicing, the splice site predictors Human Splicing Finder 3.0 [], MaxEntScan [], NNSPLICE [] and NetGene2 [] were used. To predict the biological impact of missense mutations, we looked at data from the predictor tools embedded in the N […]

library_books

Dysfunction of NaV1.4, a skeletal muscle voltage gated sodium channel, in sudden infant death syndrome: a case control study

2018
PMCID: 5899997
PMID: 29605429
DOI: 10.1016/S0140-6736(18)30021-7

[…] ere novel or with an allele frequency less than 0·00005. Variants were confirmed by Sanger sequencing using methods previously described. We assessed the effect of intronic variants on splicing using Human Splicing Finder.For mutagenesis and in-vitro transcription, we used the human SCN4A expression clone, pRc/CMV-hSkM1,, based on accession M81758.1, which we have previously used for functional e […]

call_split

Screening for germline KCNQ1 and KCNE2 mutations in a set of somatotropinoma patients

2018
PMCID: 5931228
PMID: 29703730
DOI: 10.1530/EC-18-0123
call_split See protocol

[…] mad.broadinstitute.org/) (). This database contains WGS and exome data from 138,632 individuals including 12,897 Finnish samples. Effects of the identified variants on transcripts were predicted with Human Splicing Finder (http://www.umd.be/HSF3/) () and MutationTaster (http://www.mutationtaster.org/) () online tools. Additionally, we utilized the Polyphen-2 (Polymorphism Phenotyping v2; (http://g […]

library_books

Targeted Next generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

2018
PMCID: 5933375
PMID: 29683450
DOI: 10.3791/57266

[…] disease-associated variants include any classified as likely pathogenic or pathogenic.Process splicing variants through the in silico prediction tools Splicing-based Analysis of Variants (SPANR) and Human Splicing Finder (HSF, version 3.0).If processing a large number of samples, compare the variant calls within each sample to determine which variants are shared by various samples. Do this manual […]

call_split

Full in frame exon 3 skipping of BRCA2 confers high risk of breast and/or ovarian cancer

2018
Oncotarget
PMCID: 5915120
PMID: 29707112
DOI: 10.18632/oncotarget.24671
call_split See protocol

[…] o tools: SpliceSiteFinder-like (SSF, http://www.interactive-biosoftware.com), MaxEntScan (MES, http://genes.mit.edu/burgelab/maxent/Xmaxentscan_scoreseq.html) [], NNSplice (NNS), GeneSplicer (GS) and Human Splicing Finder (HSF, http://www.umd.be/HSF/) []. These algorithms were simultaneously interrogated by using the integrated software Alamut (Interactive Biosoftware, http://www.interactive-bioso […]

library_books

The complexity of titin splicing pattern in human adult skeletal muscles

2018
PMCID: 5874998
PMID: 29598826
DOI: 10.1186/s13395-018-0156-z

[…] strument. Raw reads were mapped against the hg19 human reference genome using TopHat2 []. TopHat was also used for detecting and counting exon junctions. Alternative splice sites were evaluated using Human Splicing Finder (HSF) program [].For each exon, the inclusion rate was calculated as [(I/2)/[(I/2) + E], where I is the number of reads supporting the exon inclusion (all junctions going into an […]

Citations

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HSF institution(s)
INSERM, U827, Montpellier, France; CHU Montpellier, Hopital Arnaud de Villeneuve, Laboratoire de Genetique Moleculaire, Montpellier, France; Universite Montpellier 1, UFR Medecine, Montpellier, France
HSF funding source(s)
Supported by European Community Seventh Framework Program (FP7/2007-2013) under grant agreement number 200754—the GEN2PHEN project, the European Community Sixth Framework Program (FP6) under grant agreement number 036825 and TREAT-NMD Network of Excellence.

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