Table 1. Algorithms, parameters, and databases used in the VIROM bioinformatics pipeline
From: VIROME: a standard operating procedure for analysis of viral metagenome sequences
Process | Tool | Parameters | Subject database |
|---|---|---|---|
Screening of rRNAs | BLASTALL | -p blastn −e 1e-3 −f T − b 1 −v 1 −M BLOSUM62 |  |
Identification of tRNAs | tRNA scan SE | -b G | Â |
ORF calling | MetaGene Annotator | -m | Â |
Known protein identification | BLASTALL | -p blastp −e 1e-1 −F T − b 50 −v 50 −M BLOSUM 62 | UNIREF 100 |
Environmental Protein Identification | BLASTALL | -p blastp −e 1e-1 −F T −b 50 −v 50 −M BLOSUM62 | MGOL |