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Protocols

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 citations

 (6)
call_split

The genetic profile of Leber congenital amaurosis in an Australian cohort

2017
PMCID: 5702575
PMID: 29178642
DOI: 10.1002/mgg3.321
call_split See protocol

[…] n2 (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 ). […]

call_split

Identification of the gene defect responsible for severe hypercholesterolaemia using whole exome sequencing

2015
Sci Rep
PMCID: 4468422
PMID: 26077743
DOI: 10.1038/srep11380
call_split See protocol

[…] We used four in silico tools, the Alternative Splice Site Predictor (ASSP), Human Splice Finder (HSF), NetGene2, and Spliceman to predict the impact of C.1187-10G >A on the pre-mRNA splicing of LDLR. These software tools provide quantitative or confidence scores for the wild-type and mutant splice site sequences tha […]

library_books

RNA Binding Proteins: Splicing Factors and Disease

2015
Biomolecules
PMCID: 4496701
PMID: 25985083
DOI: 10.3390/biom5020893

[…] own to function as intronic splicing enhancers (ISEs) (A) []. Positional distribution analysis uses this property to predict loss of binding without knowledge of the trans-acting factor ([], see also Spliceman below). Non-coding, and functionally conservative or silent mutations that have little to no effect on the translated protein have been demonstrated to cause disease by disrupting splicing [ […]

call_split

Clinical and molecular characterization of a Brazilian cohort of campomelic dysplasia patients, and identification of seven new SOX9 mutations

2014
Genet Mol Biol
PMCID: 4415563
PMID: 25983619
DOI: 10.1590/S1415-475738120140147
call_split See protocol

[…] and 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 Board […]

library_books

In silico tools for splicing defect prediction A survey from the viewpoint of end users

2013
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 grou […]

call_split

TBX6, LHX1 and copy number variations in the complex genetics of Müllerian aplasia

2013
Orphanet J Rare Dis
PMCID: 3847609
PMID: 23954021
DOI: 10.1186/1750-1172-8-125
call_split See protocol

[…] 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. […]

Citations

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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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