Spliceman statistics

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Associated diseases

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Spliceman specifications

Information


Unique identifier OMICS_02259
Name Spliceman
Interface Web user interface
Restrictions to use Academic or non-commercial use
Input data A set of DNA sequences with point mutations.
Input format VCF
Output data A ranked list to predict the effects of point mutations on pre-mRNA splicing.
Programming languages Perl, PHP
Database management system PostgreSQL
Computer skills Basic
Version 2.0
Stability Stable
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/Spliceman

Taxon


  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus
    • Rattus norvegicus
  • Vertebrates
    • Danio rerio
    • Gallus gallus

Documentation


Maintainer


  • person_outline William Guy Fairbrother <>

Publications for Spliceman

Spliceman in publications

 (5)
PMCID: 5702575
PMID: 29178642
DOI: 10.1002/mgg3.321

[…] (adzhubei et al. ), and sift. splice site variants at consensus dinucleotides (±1/2) were automatically assigned a pathogenic status (hellen ; wallis et al. ) or assessed using mutation taster and spliceman (lim and fairbrother )., between 1 june 2001 and 31 december 2015, 50 individuals with a clinical diagnosis of lca from 40 unrelated pedigrees were enrolled into the airdr […]

PMCID: 4468422
PMID: 26077743
DOI: 10.1038/srep11380

[…] by c.1187-10g >a. the quantitative or confidence scores of the cryptic donor site are higher than the natural site according to the four software tools (). the l1 distance calculated with spliceman was 37994 with a percentile rank of 82%, which represents a high possibility that the c.1187-10g >a disrupts splicing., we genotyped the cdna of ldlr in the nuclear family. the proband […]

PMCID: 4415563
PMID: 25983619
DOI: 10.1590/S1415-475738120140147

[…] y chromosome-specific sequences in zinc finger protein, x-linked (zfx), and sex determining region y (sry) genes, respectively. primer sequences and pcr conditions are available upon request. the spliceman web server () was used to estimate the pathogenicity of the splice-site mutation identified in patient 3., ethical approval for this study was obtained from both the institutional review […]

PMCID: 4029872
PMID: 24263461
DOI: 10.1038/gim.2013.176

[…] cryp-skip (http://cryp-skip.img.cas.cz/): multiple logistic regression model which distinguishes exons that are skipped and that activate cryptic splice sites as a result of splicing mutations; and spliceman (http://fairbrother.biomed.brown.edu/spliceman/index.cgi): prediction of how likely distant mutations around annotated splice sites disrupt splicing by clustering hexamers into distinct […]

PMCID: 3847609
PMID: 23954021
DOI: 10.1186/1750-1172-8-125

[…] in silico analyses of genomic variants were performed using mutationtaster [], pon-p [] including phd-snp 2.0.6, polyphen 2.0.22, sift 4.0.3, snap 1.0.8 and i-mutant 3.0.6 programs used for analysis, spliceman [], spliceport [] and human splicing finder [] software programs., initially, we chose 50 patients for copy number analysis using acgh and identified nine cnvs in eight (16%) of them (table  […]


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Spliceman institution(s)
Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, USA; Center for Computational Molecular Biology, Brown University, Providence, RI, USA; Division of Applied Mathematics, Brown University, Providence, RI, USA; Hassenfeld Child Health Innovation Institute, Brown University, Providence, RI, USA
Spliceman funding source(s)
The National Institute of Health (1R01GM095612-01)

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