NAME

       stranslate - translate a nucleic acid sequence to protein ORFs

SYNOPSIS

       stranslate [-options] <seqfile>

DESCRIPTION

       This manual page documents briefly the stranslate command.

       stranslate  is  a program that creates a file of all possible protein ORFs, given an input
       nucleic acid sequence.

OPTIONS

       Available options:

       -a     Translate in full, with stops; no individual ORFs.

       -h     Help; show brief usage and version info.

       -l <minlen>
              Report only ORFs greater than minlen (default 20).

       -m     Require ORFs to start with AUG/Met.

       -o <outfile>
              Save results in output file.

       -q     Quiet; silence banner, for piping or redirection.

       -s <stopchar>
              With -a, set stop character to <stopchar>.

       --tetrahymena
              Use the Tetrahymena/Oxytricha genetic code.

       --watson
              Only do the top strand (frames 0/1/2).

       --crick
              Only do the bottom strand (frames 3/4/5).

NOTE TO DEBIAN USERS

       The original program name is translate. It was renamed to  stranslate  to  avoid  conflict
       with another program of the same name.

SEE ALSO

       afetch(1),  alistat(1),  compalign(1), compstruct(1), revcomp(1), seqsplit(1), seqstat(1),
       sfetch(1), shuffle(1), sindex(1), sreformat(1), weight(1).

AUTHOR

       Sean Eddy
       HHMI/Department of Genetics
       Washington University School of Medicine
       4444 Forest Park Blvd., Box 8510
       St Louis, MO 63108 USA
       Phone: 1-314-362-7666
       FAX  : 1-314-362-2157
       Email: eddy@genetics.wustl.edu

       This manual page was written by Nelson A. de Oliveira <naoliv@gmail.com>,
       for the Debian project (but may be used by others).

                                 Mon, 01 Aug 2005 15:28:08 -0300                    STRANSLATE(1)