GaoyangLuo / RdRp-scan

Exploring the "dusk matter" of the RNA virosphere

RdRp-Scan - Exploring the "dusk matter" of the RNA virosphere

RdRp sequence database

• RdRp-scan_0.90.info : List of accessions, taxonomy, viral species and putative host of RdRp-scan entries
• RdRp-scan_0.90.fasta : RdRp-scan RdRp core protein sequence database in fasta format
• RdRp-scan_0.90.dmnd : RdRp-scan RdRp core protein sequence database in diamond format (v.2.0.9)

RdRp motif database (Motif_db)

• {viral_order}.RdRp_motifs.fasta : RdRp motif sequences for each viral taxa

RdRp phylogenies (Phylogenies)

• {viral_phyla}.CLUSTALO_0.4.fasta : RdRp-alignments for each individual taxa (Clustal-omega)
• RdRp-scan.CLUSTALO_0.4.fasta : RdRp-alignment used to build the master RdRp tree (Clustal-omega)
• RdRp-scan.CLUSTALO_0.4.FAST_TREE : RdRp FastTREE file in Newick format

HMM-RdRp database (Profile_db_and_alignments)

• RdRp_HMM_profile.db.h3? : RdRp HMM profile database (Hmmer3-compatible ; v3.3)
• {viral-taxa}HMM_CLUSTALO.0.4.fasta : Clustal-omega alignments (40% identity cut-off) used to build HMM profiles.

PDB_virRdRp_acc.txt : list of viral RdRp PDB accessions
RdRp_keyword.list : list of keyword used to retrieve RdRp-like accessions from NCBI Genbank
RdRp_InterPro_keyword.list : list of viral RdRp-like InterProScan entries

RdRp-scan Workflow