stranslate

Langue: en

Version: 252070 (debian - 07/07/09)

Section: 1 (Commandes utilisateur)

Sommaire

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).