Tag: Splicing

IntSplice 1.1 – Prediction of the Splicing Consequences of Intronic Single-nucleotide Variations in the Human Genome

IntSplice 1.1

:: DESCRIPTION

IntSplice is a tool to predict a splicing consequence of an SNV at intron positions -50 to -3 close the 3’ end of an intron of the human genome.

::DEVELOPER

IntSplice team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

IntSplice: prediction of the splicing consequences of intronic single-nucleotide variations in the human genome.
Shibata A, Okuno T, Rahman MA, Azuma Y, Takeda JI, Masuda A, Selcen D, Engel AG, Ohno K.
J Hum Genet. 2016 Mar 24. doi: 10.1038/jhg.2016.23.

PULSE – Positive Unlabeled Learning for Splicing Elucidation

PULSE

:: DESCRIPTION

PULSE is a semi-supervised learning algorithm, positive unlabeled learning for splicing elucidation, which uses 48 features spanning various categories.

::DEVELOPER

Kim Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX

:: DOWNLOAD

 PULSE

:: MORE INFORMATION

Citation

Cell Rep. 2015 Jul 14;12(2):183-9. doi: 10.1016/j.celrep.2015.06.031. Epub 2015 Jul 2.
Semi-supervised Learning Predicts Approximately One Third of the Alternative Splicing Isoforms as Functional Proteins.
Hao Y, Colak R, Teyra J, Corbi-Verge C, Ignatchenko A, Hahne H, Wilhelm M, Kuster B, Braun P, Kaida D, Kislinger T, Kim PM

ALTSCAN 1.0 – ALTernative Splicing SCANner

ALTSCAN 1.0

:: DESCRIPTION

ALTSCAN is an ab initial alternative splicing predictor whose primary purpose is to explore protein-coding structures as many as possible.

::DEVELOPER

Dr. Chaochun Wei

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 ALTSCAN

:: MORE INFORMATION

Citation

Hu, Z., Scott, H., Qin, G., Zheng, G, Chu, X., Xie, L., Adelson, D., Oftedal, B., Venugopal, P., Babic, M., Hahn, C., Zhang, B., Wang, X., Li, N., Wei, C.*,
Revealing missing human protein isoforms based on ab initio prediction, RNA-seq and proteomics
Scientific Reports, 2015, 5:10940.

ESEfinder 3.0 – Exon Splicing Enhancer Finder

ESEfinder 3.0

:: DESCRIPTION

ESEfinder is a web-based resource that facilitates rapid analysis of exon sequences to identify putative ESEs responsive to the human SR proteins SF2/ASF, SC35, SRp40 and SRp55, and to predict whether exonic mutations disrupt such elements.

::DEVELOPER

ESEfinder team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Smith, P. J., Zhang, C., Wang, J. Chew, S. L., Zhang, M. Q. and Krainer, A. R. 2006.
An increased specificity score matrix for the prediction of SF2/ASF-specific exonic splicing enhancers.
Hum. Mol. Genet. 15(16): 2490-2508.

Cartegni L., Wang J., Zhu Z., Zhang M. Q., Krainer A. R.; 2003.
ESEfinder: a web resource to identify exonic splicing enhancers.
Nucleic Acid Research, 2003, 31(13): 3568-3571.

SpliceJumper – Splicing Junction Calling from RNA-Seq data

SpliceJumper

:: DESCRIPTION

SpliceJumper is a classification based approach for calling splicing junctions from RNA-seq data

::DEVELOPER

Simon C Chu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SpliceJumper

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2015;16 Suppl 17:S10. doi: 10.1186/1471-2105-16-S17-S10. Epub 2015 Dec 7.
SpliceJumper: a classification-based approach for calling splicing junctions from RNA-seq data.
Chu C, Li X, Wu Y.

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