Palmscan algorithm

Palmscan is software to detect viral polymerase palmprint barcode sequences in longer sequences such as virus genomes and ORFs. Palmprints can be used to classify RNA viruses.

PALMdb is a database of palmprint sequences generated by mining public databases with palmscan.

Palmprint sequence

Repository layout

palmscan/
  src/               # Source code (C++)
  bin/               # Pre-built binaries for Linux and Windows
  motif_msas/        # Multiple alignments used to train PSSMs
  test/data          # Test data
  test/results       # Test results
  test/runtest.bash  # Script to run tests

Software usage

Example command line:

palmscan -search_pp inputfile.fa -rt -rdrp -ppout pp.fa -report pp.txt -fevout pp.fev

Type palmscan -help for option details.

Reference

A. Babaian and R. C. Edgar (2021), Ribovirus classification by a polymerase barcode sequence (2021), biorxiv https://doi.org/10.1101/2021.03.02.433648