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) |