Examples of splice site, SRE, and BP prediction tools Examples of splice site, SRE, and BP prediction tools Examples of splice site, SRE, and BP prediction tools Examples of splice site, SRE, and BP prediction tools
Tool Motifs References Web User Interface
Human Splicing Finder (HSF) 5’ and 3’ splice site motifs, SRE, BP Desmet et al. (2009) http://www.umd.be/HSF/
MaxEntScan (MES) 5’ and 3’ splice site motifs Yeo and Burge (2004) http://hollywood.mit.edu/burgelab/maxent/Xmaxentscan_scoreseq.html
Splice Site Finder 5’ and 3’ splice site motifs Shapiro and Senapathy (1987) N/A
SPiCE 5’ and 3’ splice site motifs Leman et al. (2018) N/A
MES-based VEP plugin 5’ and 3’ splice site motifs Shamsani et al. (2018) N/A
ΔtESRseq SRE Di Giacomo et al. (2013) N/A
ΔHZEI SRE Erkelenz et al. (2014) https://www2.hhu.de/rna/html/hexplorer_score.php
ΔΨ SRE Xiong et al. (2015) N/A
EX-SKIP SRE Raponi et al. (2011) http://ex-skip.img.cas.cz/
HOT-SKIP SRE Raponi et al. (2011) https://hot-skip.img.cas.cz/
Branchpointer BP Signal et al. (2018) N/A
LaBranchoR BP Paggi and Bejerano (2018) http://bejerano.stanford.edu/labranchor/
SVM-BPfinder BP Corvelo et al. (2010) http://regulatorygenomics.upf.edu/Software/SVM_BP/
Branch Point Prediction (BPP) BP Q. Zhang et al. (2017) N/A
RNA Branch Point Selection (RNABPS) BP Nazari, Tayara, and Chong (2019) https://home.jbnu.ac.kr/NSCL/rnabps.htm
SRE algorithms in Human Splicing Finder v3.1 SRE algorithms in Human Splicing Finder v3.1 SRE algorithms in Human Splicing Finder v3.1 SRE algorithms in Human Splicing Finder v3.1
Type of Signal Prediction Algorithm Prediction Algorithm References
ESE HSF: 9G8, Tra2-β HSF: 9G8, Tra2-β Desmet et al. (2009)
ESEfinder: SF2/ASF, SF2/ASF(IgM), SC35, SRp40, SRp55 ESEfinder: SF2/ASF, SF2/ASF(IgM), SC35, SRp40, SRp55 Cartegni, Wang, Zhu, Zhang, and Krainer (2003)
RESCUE ESE hexamers RESCUE ESE hexamers Fairbrother, Yeh, Sharp, and Burge (2002)
ESS HSF hnRNP-A1 HSF hnRNP-A1 Desmet et al. (2009)
Sironi motifs Sironi motifs Sironi et al. (2004)
ESS decamers ESS decamers Z. Wang et al. (2004)
ESE and ESS PESX Octamers PESX Octamers X. H.-F. Zhang and Chasin (2004)
ESR Sequences ESR Sequences Goren et al. (2006)
EIEs & IIEs Hexamers EIEs & IIEs Hexamers C. Zhang, Li, Krainer, and Zhang (2008)