Table 1. Third party tools, cutoffs, and parameters used in this pipeline
From: The JCVI standard operating procedure for annotating prokaryotic metagenomic shotgun sequencing data
Process | Function | Tool | Parameters |
|---|---|---|---|
Structural Annotation | Â | Â | Â |
| Â | tRNA identification | tRNAscan-SE (1.23) | tRNAscan-SE -q -b -G |
|  | ncRNA finder stage 1 | BLAST | blastall -p blastn -i -d -e 0.1 -F ″T″-b 1 -v 1 -z 3000000000 -W 9 |
|  | ncRNA finder stage 2 | BLAST | blastall -p blastn -i -d -e 1e-4 -F ″m L″-b 1500 -v 1500 -q -5 -r 4 -X 1500 -z 3000000000 -W 9 -U T |
| Â | Protein Identification | MetaGeneAnnotator | -m |
Functional Annotation | Â | Â | Â |
|  | Protein annotation | BLAST | blastall -p blastp -v 10 -b 10 -X 15 -e 1e-5 -M BLOSUM62 -J F -K 10 -f 11 -Z 25.0 -W 3 -U F -I F -E -1 -y 7.0 -G -1 -A 40 -Y 0.0 -F ″T″ -g T -d -i -o -z 1702432768 -m 7 |
| Â | Protein annotation | hmmpfam | Â |
| Â | Protein annotation | lipoprotein_motif | --is_micoplasm 0 |
| Â | Protein annotation | tmhmm | Â |
| Â | EC assignment | PRIAM | rpsblast -i -d -m 8 -e 1e-10 |