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Palmscan is obsolete

Palm_annot is recommended, it is based on HMMs and has much better sensitivity and much lower false-positive rate compared to the PSSMs in Palmscan.

https://github.com/rcedgar/palm_annot

palmscan

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

Polymerase structure

Repository layout

palmscan/
  src/               # Source code (C++)
  test/data          # Test data
  test/results       # Test results
  test/runtest.bash  # Script to run tests

Software usage

Example command line:

palmscan2 -search_pssms seqs.fasta -tsv hits.tsv

Type palmscan -help for option details.

Reference

A. Babaian and R. C. Edgar (2022), Ribovirus classification by a polymerase barcode sequence, PeerJ. https://peerj.com/articles/14055/

R. C. Edgar et al. (2021), Petabase-scale sequence alignment catalyses viral discovery, Nature 2022 https://www.nature.com/articles/s41586-021-04332-2
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