Skip to main content

Table 4. Software versions and parameters

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