PalmDB
PalmDB home
Downloads
Data sources
Viral RdRp
Barcodes
Palmprint+core
RdRp barcodes
Search methods
Publications

RdRp search methods


palm_annot
Primary search and annotation method for PalmDB
https://github.com/rcedgar/palm_annot

Interpro (PFAM) HMMs
https://www.ebi.ac.uk/interpro/search/text/viral%20rdrp/?page=1#table
    PF00680: RdRP_1
    PF00978: RdRP_2
    PF00998: RdRP_3
    PF02123: RdRP_4
    PF07925: RdRP_5
    PF00946: Mononeg_RNA_pol
    PF03431: RNA_replicase_B
    PF04196: Bunya_RdRP
    PF04197: Birna_RdRP
    PF05919: Mitovir_RNA_pol
    PF00972: Flavi_NS5
RdRp-scan HMMs
https://github.com/JustineCharon/RdRp-scan
https://doi.org/10.1093/ve/veac082

Zayed2020 HMMs
https://zenodo.org/record/5731488
https://doi.org/10.1126/science.abm5847

Palmscan-v1 PSSMs
https://github.com/rcedgar/palmscan
https://doi.org/10.7717/peerj.14055

Palmscan-v2 PSSMs
https://github.com/rcedgar/palmscan2

NeoRdRp HMMs
https://github.com/shoichisakaguchi/NeoRdRp
https://www.jstage.jst.go.jp/article/jsme2/37/3/37_ME22001/_article

Luca language model AI
Hou2023