Palmdb

Current Release: 2023-04-26. sOTU count: 508,607

• palmdb is a database of viral polymerase palmprint (barcode) sequences classified by clustering sequences into species-like operational taxonomic units (OTUs) at 90% amino acid identity.
• palm_annot (link) is a command-line tool to identify RdRp sequences and annotate the palmprints within them.
• palmID (link) is a web-tool to query palmdb with an RdRp sequence, and retrieve matches in the SRA.

The hallmark gene for RNA viruses is the RNA-dependent RNA-polymerase (RdRp). Palmprints are a ~100aa sub-sequence of RdRp delineated by the conserved catalytic motifs "A", "B", and "C" in the palm sub-domain.

Learn more...

Download

• Release: palmdb.current.tar.gz (4 GB)

Palmprint sequences

• sOTU palmprints: sotus.palmprint.faa (63 MB)
• all-unique palmprints, unclustered: unique.palmprint.faa (131.3 MB)
• sOTU source labels: label_sotu.tsv (178.2 MB)

RdRp sequences

Source-original sequences are avaialble in the raw/ folder of the Current Release

References

• Babaian and Edgar, 2022. Ribovirus classification by a polymerase barcode sequence. PeerJ

• Edgar et al., 2022. Petabase-scale sequence alignment catalyses viral discovery. Nature