Table 2.

Prediction algorithms for the analysis of splicing effect

Prediction of splice sites
NetGene2	http://www.cbs.dtu.dk/services/NetGene2/	Hebsgaard et al. (1996), Brunak et al. (1991)
Splice Site Prediction by Neural Network	www.fruitfly.org/seq_tools/splice.html	Reese et al. (1997)
SplicePredictor	http://brendelgroup.org/bioinformatics2go/SplicePredictor.php	Brendel et al. (2004)
Splice port	http://spliceport.cbcb.umd.edu/	Dogan et al. (2007)
SpliceView	http://bioinfo.itb.cnr.it/oriel/splice-view.html	Shapiro and Senapathy (1987), Rogozin and Milanesi (1997)
Analyzer Splice Tool	http://ibis.tau.ac.il/ssat/SpliceSiteFrame.htm	Carmel et al. (2004)
GENSCAN	http://genes.mit.edu/GENSCAN.html	Burge and Karlin (1997)
GeneSplicer	http://www.cbcb.umd.edu/software/GeneSplicer/gene_spl.shtml	Pertea et al. (2001)
MaxEntScan	http://genes.mit.edu/burgelab/maxent/Xmaxentscan_scoreseq.html	Yeo and Burge (2004)
Spliceman	http://fairbrother.biomed.brown.edu/spliceman/	Lim et al. (2011), Lim and Fairbrother (2012)
CRYP-SKIP	http://cryp-skip.img.cas.cz/	Divina et al. (2009)
SROOGLE	http://sroogle.tau.ac.il/	Schwartz et al. (2009)
Human Splicing Finder	www.umd.be/HSF/	Desmet et al. (2009)
MutPredSplice	http://www.mutdb.org/mutpredsplice/submit.htm	Mort et al. (2014)
Alamut Visual Software	http://www.interactive-biosoftware.com	Interactive Biosoftware
MutationForecaster	https://mutationforecaster.com/index.php	CytoGnomix® Inc.
Prediction of branch site and polypyrimidine tract
Branch Site Analyzer	http://ibis.tau.ac.il/ssat/BranchSite.htm	Kol et al. (2005)
SVM-BPfinder	http://regulatorygenomics.upf.edu/Software/SVM_BP/	Corvelo et al. (2010)
IntSplice	https://www.med.nagoya-u.ac.jp/neurogenetics/IntSplice/	Shibata et al. (2016)
Variant annotations
Variant Effect Predictor tool	https://www.ensembl.org/info/docs/tools/vep/index.html	Ensembl release 91—December 2017© EMBL-EBI
Alamute Batch software	http://www.interactive-biosoftware.com/alamut-batch/
Prediction of ESE or ESS
ESEfinder	http://exon.cshl.org/ESE	Cartegni et al. (2003), Smith et al. (2006)
RESCUE-ESE programs	http://genes.mit.edu/burgelab/rescue-ese/	Fairbrother et al. (2002)
HEXplorer score	https://www2.hhu.de/rna/html/hexplorer_score.php	Erkelenz et al. (2014)
ESRsearch	http://esrsearch.tau.ac.il/	Goren et al. (2006), Fairbrother et al. (2002), Zhang and Chasin (2004)
FAS-ESS	http://genes.mit.edu/fas-ess/	Wang et al. (2004)
SpliceAid2	http://193.206.120.249/splicing_tissue.html	Piva et al. (2012)
SPANR tool	http://tools.genes.toronto.edu/	Xiong et al. (2015)
EX-SKIP	http://ex-skip.img.cas.cz/	Raponi et al. (2011)
HOT-SKIP	http://hot-skip.img.cas.cz/	Raponi et al. (2011)
Prediction of mRNA secondary structure
mFold	http://unafold.rna.albany.edu/?q=mfold	Zuker (2003)
pFold	http://daimi.au.dk/~compbio/pfold/	Knudsen and Hein (2003)