justinecharon/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

rdrp-scan's Issues

FATAL: Tree::GetToken: input buffer too small, token so far='JAAOEH01000077'

Hi, I try to align my sequence to RdRp-scan.CLUSTALO_0.4.fasta, but I met the issue below. how to resolve it?
clustalo -i target_sequences.fasta --guidetree-in=RdRp-scan.CLUSTALO_0.4.fasta -o aligned_sequences.fasta

RdRp_HMM_profile.db.h3?

Thank you for developing this useful data resource. I could not find RdRp_HMM_profile.db.h3? in Profile_db_and_alignments, but RdRp_HMM_profile_CLUSTALO.db.h3? files are there. Is this because of the typo?

How to run the step 7 motif detection?

I have finished to run the first 6 steps. How can I run the step 7: detect A,B,C motifs using RDRP motif database? What output will be generated? Thank you!

Inconsistency in numbers of RdRp-scan.CLUSTALO_0.4.fasta and RdRp-scan.CLUSTALO_0.4.FAST_TREE

Hi, when I try to get lables of RdRp-scan.CLUSTALO_0.4.FAST_TREE with "nw_labels RdRp-scan.CLUSTALO_0.4.fasta", It run wrong. So I upload RdRp-scan.CLUSTALO_0.4.FAST_TREE to iTol, and then download a new newick file.
Then I found that RdRp-scan.CLUSTALO_0.4.fasta has 3409 sequences, and RdRp-scan.CLUSTALO_0.4.FAST_TREE_iTol has 3382, It appears that 27 sequences were lost. This may be due to the different parsing capabilities of iTol and nw_labels. Do you have a way to make it the same size?