CHECKTRANS(1e) | EMBOSS Manual for Debian | CHECKTRANS(1e) |
NAME¶
checktrans - Reports STOP codons and ORF statistics of a proteinSYNOPSIS¶
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 seqallRequired section¶
-orfml integerDefault value: 100
Additional section¶
-addlast booleanAn 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.
05/11/2012 | EMBOSS 6.4.0 |