Version: v1.0
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
.
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
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.
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