Viruses and CRISPR · What you can do here
Find RNA viruses in metatranscriptome assemblies
Identify RNA viruses in metatranscriptome assemblies by screening for RdRp domains across eight profile HMM collections, with MMseqs2 taxonomy against RefSeq RNA viruses.
What this involves
Metatranscriptomic discovery of RNA viruses centres on the RNA-dependent RNA polymerase (RdRp), the sole universally conserved gene shared across Orthornavirae. General viral marker tools are tailored primarily to DNA viruses, so uncovering RNA viruses in metatranscriptomes, host transcriptomes, or protein sets requires targeted profile hidden Markov model searches against RdRp domains.
The platform agent executes RdRpCATCH via the find_rna_viruses tool on its own dedicated machine, querying input contigs against eight published RdRp profile collections simultaneously. It performs taxonomic placement using MMseqs2 against RefSeq RNA viruses and extracts candidate RdRp protein sequences directly into a results directory, with no local software setup required.
Evaluating candidate viruses requires assessing profile coverage, the number of matching profile collections, and the exact taxonomic rank supported by lowest common ancestor analysis. Because sequence data alone does not establish host identity, and atypical genetic codes can alter open reading frames, proper classification depends on examining the evidence behind each hit.
How it goes
- 1Input sequence provisionProvide metatranscriptome contigs as an NCBI nucleotide accession, a download URL, or a local FASTA file path on the machine, in plain or gzipped format.
- 2Profile HMM screeningThe agent runs find_rna_viruses (RdRpCATCH) to search your sequences against eight published RdRp profile collections at once.
- 3Taxonomic placementRdRpCATCH runs MMseqs2 against RefSeq RNA viruses and applies a two-step lowest common ancestor method to assign taxonomy down to the rank supported by the data.
- 4Protein sequence extractionThe agent collects the extracted RdRp protein sequences from the output directory so they are ready for multiple alignment and phylogenetic analysis.
Start it here
Ask in plain language. The agent works on a Linux machine of its own — it installs and runs what the job needs, keeps every file, and reads the results back with the numbers explained. Nothing to set up, and a long run continues after you close the page.
What to watch for
- A hit from only one profile collection with partial coverage remains merely a candidate, whereas full profile coverage across five collections confirms an RdRp.
- Host identity cannot be determined from the sequence alone; a viral contig found in an insect sample may stem from gut contents, a parasite, or ingested plant material.
- Mitoviruses read the UGA codon as tryptophan, so you must scan with genetic_code 4 to avoid truncated translations.
- Endogenous viral elements (EVEs) can masquerade as active RNA viruses when RdRp-like fragments appear in DNA-derived datasets or inside host-length contigs.
- Sequence identity below roughly 90% amino-acid identity to an RdRp reference is commonly termed a putative new species, but you must label it putative because ICTV criteria vary by family.
What it runs
Questions
Do I need to install anything to find rna viruses in metatranscriptome assemblies?
No. The research agent does this work on a Linux machine of its own — it runs RdRpCATCH there, keeps the files, and reads the results back to you. Long runs continue if you close the page.
Why use RdRpCATCH instead of a general tool like geNomad?
geNomad's marker sets are strongest on DNA viruses, whereas RdRpCATCH screens specifically for the RNA-dependent RNA polymerase found in all Orthornavirae RNA viruses.
How does the tool classify novel viral sequences?
It runs MMseqs2 against RefSeq RNA viruses using a two-step lowest common ancestor procedure that stops at the highest taxonomic rank the evidence supports, such as Lenarviricota.
Which RNA virus lineages represent bacteriophages?
Only Leviviricetes and Cystoviridae are known RNA phages; mitoviruses and narnaviruses occupy fungal or plant organelles and cytoplasm, and nearly all other RNA viruses infect eukaryotes.
Written from the method the research agent follows for this work and the documentation of the tools listed above. Statements citing a figure that does not appear there are removed before publication. Corollary is a non-commercial research demonstration; results are not for clinical use.