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