Table 1.

Bioinformatics tools for branch point analyses, Human Splicing Finder (HSF), SVM-BPfinder, Branch Point Prediction (BPP), Branchpointer, LaBranchoR, RNA Branch Point Selection (RNABPS), with their main features and their accessibility

Tools	Features	Input	Accessibility	Refs
HSF	• Position weighted matrix of 7-mers (YNYCRAY)	DNA sequences1 or variants1 (nomenclature HGVS2)	Available as a web-application http://www.umd.be/HSF3/	[14]
	• Train on conserved sequences from the Ensembl transcripts
SVM-BPfinder	• Support vector machine combining BP predictions and PPT3 features	DNA sequences (between 20 and 500 nt length)	Available as a web-application + Perl script http://regulatorygenomics.upf.edu/Software/SVM_BP/	[15]
	• Train on conserved sequences from 7 mammalian species (with Human)
BPP	• Mixture model combining BP predictions and PPT3 features	DNA sequences (unlimited sequence length)	Available as a python script https://github.com/zhqingit/BPP	[18]
	• Train on conserved sequences from human introns
Branchpointer	• Machine learning taking into account the primary and secondary structure of the RNA molecule	Text files with genomic coordinates (format defined by Branchpointer)	Available as an R Bioconductor package https://www.bioconductor.org/packages/release/bioc/html/branchpointer.html	[19]
	• Train on high-confidence BPs [10]
LaBranchoR	• Deep learning based on bidirectional LSTM4 network	DNA sequences (70 nt upstream of the di-nucleotide AG)	Available as a python script + UCSC genome browser http://bejerano.stanford.edu/labranchor/	[20]
	• Train on high-confidence BPs [10]
RNABPS	• Deep learning based on dilated convolution and bidirectional LSTM4 network	DNA sequences (70 nt upstream of the di-nucleotide AG)	Available as a web-application https://home.jbnu.ac.kr/NSCL/rnabps.htm	[21]
	• Train on high-confidence BPs [10] plus [16]

¹ Batch analyses are not available; ² HGVS Human Genome Variation Society [22], https://varnomen.hgvs.org/; ³ PPT PolyPyrimidine Tract; ⁴ LSTM Long Short-Term Memory