From: The IGS Standard Operating Procedure for Automated Prokaryotic Annotation
Section | Tool | Version | Parameters |
---|---|---|---|
Structural | tRNA-scanSE | 1.23 | -q -b -B |
Annotation | RNAmmer | 1.2 | -S bac -m lsu,tsu,ssu, -xml -gff |
 | Glimmer3 | 3.02 | -o50 -g110 -t30 -z11 -l -X |
Functional | blastall -p blastx | 2.2.17 | -e 1e-5 -F T -b 150 -v 150 -M BLOSUM62 |
Annotation | HMMer | 2.3.2 | -acc |
 | SignalP | 3.0b | -m ‘nn+hmm’ -trnc 1000 -graphics ‘gif+eps’ |
 | TMHMM | 2.0c | --libdir TMHMM/lib |
 | LipoP | 1.0a | -short -cutoff -3 |
 | Prosite (ps_scan) | 1.34 | -s |
 | RPS-blast | 2.2.17 | -e 1e-5 -F T -b 150 -v 150 |
 | Blastp | 2.2.17 | -e 1e-5 -F T -b 150 -v 150 -M BLOSUM62 |