SplicePort protocols

View SplicePort computational protocol

SplicePort statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left Splicing defect prediction chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

SplicePort specifications

Information


Unique identifier OMICS_10857
Name SplicePort
Interface Web user interface
Restrictions to use None
Input data DNA/RNA sequence
Input format FASTA
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Rezarta Islamaj Dogan <>

Publication for SplicePort

SplicePort in pipelines

 (2)
2016
PMCID: 5030299
PMID: 27708576
DOI: 10.3389/fnagi.2016.00220

[…] the effects of these variants were evaluated with several types of predictive software, including (1) mutationtaster (http://www.mutationtaster.org/); (2) mutalyzer (https://mutalyzer.nl/); (3) spliceport (http://spliceport.cbcb.umd.edu), (4) alternative splice site predictor (assp) (http://wangcomputing.com/assp/index.html), and (5) human splicing finder (http://www.umd.be/hsf/). finally, […]

2015
PMCID: 4795202
PMID: 25758993
DOI: 10.1038/ejhg.2015.38

[…] were evaluated for pathogenicity using polyphen-2 v2.2.2 and sift. sequence variants that aligned within annotated splice sites were evaluated with online web services human splice finder v2.4.1, spliceport and alternative splice site prediction. refseq nm_001203.2 was used as input sequence for all of the prediction services. sequence variants were deposited at http://databases.lovd.nl/. […]


To access a full list of citations, you will need to upgrade to our premium service.

SplicePort in publications

 (44)
PMCID: 5520924
PMID: 28617436
DOI: 10.1038/cddis.2017.269

[…] on human cancer databases, including cosmic, cbioportal, as well as in dbsnp and 1000 genomes. the minor allele frequency in the exac database is 3.533e−5 (4/113218). bioinformatic predictions using spliceport, genesplicer and mutationtaster uniformly indicated that a new acceptor splice site would be created due to this single base exchange., to confirm whether alternative splice transcripts […]

PMCID: 5499207
PMID: 28604674
DOI: 10.1038/ncomms15824

[…] this deep intronic rare variant is predicted by spliceaid2 (ref. ) to create multiple binding sites for splice enhancers. together with the correctly predicted new acceptor and donor sites by spliceport (feature generation algorithm score 0.112 and 1.308, respectively) this emphasizes the influence of this variant in the creation of the new exon. besides, the four other tools predicted […]

PMCID: 5686667
PMID: 29264534
DOI: 10.1210/js.2017-00124

[…] sequences. it is a purine (a) to pyrimidine (c) substitution at the end of a polypyrimidine tract 2 bp upstream of the canonical splice acceptor site ag. we performed in silico analysis by using spliceport [], which makes splice-site predictions based on a collection of 4000 pre-messenger rna (mrna) human refseq sequences using a feature generation algorithm. the result suggested […]

PMCID: 5356018
PMID: 28303972
DOI: 10.1038/srep44775

[…] have been deleted to render them dysfunctional, should any transcription initiate from a cryptic promoter. potential splice sites and polyadenylation sequences were identified and removed using spliceport. the stuffer was synthesised by and purchased from genscript (nj, usa)., for nigw viruses, vsv-g-pseudotyped lentiviral vectors were produced by co-transfecting 6 × 106 hek 293t cells […]

PMCID: 5427806
PMID: 28250438
DOI: 10.1038/s41598-017-00152-5

[…] have been deleted to render them dysfunctional, should any transcription initiate from a cryptic promoter. potential splice sites and polyadenylation sequences were identified and removed using spliceport. the stuffer was synthesised by and purchased from genscript (nj, usa)., for nigw viruses, vsv-g-pseudotyped lentiviral vectors were produced by co-transfecting 6 × 106 hek 293t cells […]


To access a full list of publications, you will need to upgrade to our premium service.

SplicePort institution(s)
Computer Science Department, University of Maryland, College Park, MD, USA; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA; Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA
SplicePort funding source(s)
Supported by the National Center for Biotechnology Information (NCBI) Scientific Visitors Program sponsored by the National Library of Medicine and administered by the Oak Ridge Institute for Science and Education, and by the National Science Foundation under grant number 0544309.

SplicePort reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review SplicePort