NAME

       checktrans - Reports STOP codons and ORF statistics of a protein

SYNOPSIS

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

       checktrans -help

DESCRIPTION

       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

BUGS

       Bugs can be reported to the Debian Bug Tracking system (http://bugs.debian.org/emboss), or
       directly to the EMBOSS developers
       (http://sourceforge.net/tracker/?group_id=93650&atid=605031).

SEE ALSO

       checktrans is fully documented via the tfm(1) system.

AUTHOR

       Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
           Wrote the script used to autogenerate this manual page.

COPYRIGHT

       This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package.
       It can be redistributed under the same terms as EMBOSS itself.