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checktrans - Reports STOP codons and ORF statistics of a protein


checktrans -sequence seqall -orfml integer [-addlast boolean] -outfile outfile
-outseq seqoutall -outfeat featout

checktrans -help


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


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

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