I built a simple tool that maps splicing regulatory elements onto genomic DNA sequences and writes color-coded annotations back to the GenBank file, viewable in SnapGene or UGENE.

GitHub: https://github.com/maxwraae/splicemap

Given a GenBank file with exon annotations, it annotates:

• Splice sites (MaxEntScan)
• Branch points (BPP + SVM-BPfinder, top candidates from both)
• Polypyrimidine tract (length, pyrimidine %, longest U-run)
• Exonic splicing enhancers (ESEfinder for SR protein binding, ESRseq for functional hexamer scores)

• Exonic splicing silencers (hnRNP motifs, ESRseq negative scores)

  It also generates a markdown report with scores and a terminal summary.

  1. pip install -r requirements.txt
  2. Download your gene as a RefSeqGene from NCBI Gene (https://www.ncbi.nlm.nih.gov/gene/)
  3. python splicemap.py splicemap gene.gb -t <transcript accession>

Any feedback on the tool, the methods, or what's missing would be welcome.