checktrans1e
Reports stop codons and orf statistics of a protein
Usage
checktrans -sequence
seqall
-orfml
integer
[-addlast
boolean]
-outfile
outfile
-outseq
seqoutall
-outfeat
featout
checktrans -help
Overview
checktrans is a command line program from EMBOSS (“the European Molecular Biology Open Software Suite”). It is part of the "Nucleic:Gene finding,Nucleic:Translation" command group(s).
Options
Input section
-
-sequence seqall
Required section
-
-orfml integer -
Default value: 100
Additional section
-
-addlast boolean -
An asterisk in the protein sequence indicates the position of a STOP codon. Checktrans assumes that all ORFs end in a STOP codon. Forcing the sequence to end with an asterisk, if there is not one there already, makes checktrans treat the end as a potential ORF. If an asterisk is added, it is not included in the reported count of STOPs. Default value: Y
Output section
-
-outfile outfile
-
-outseq seqoutall -
Sequence file to hold output ORF sequences
-
-outfeat featout -
File for output features
Releases
9 releases since Debian 5.0 (Lenny); the text changed 2 times.