revcomp(1) [debian man page]

REVCOMP(1)						      General Commands Manual							REVCOMP(1)

NAME

       revcomp - reverse complement a nucleic acid sequence

SYNOPSIS

       revcomp [-options] <seqfile>

DESCRIPTION

       This manual page documents briefly the revcomp command.

       revcomp is a program that generates reverse complement of sequences.

OPTIONS

       Available options:

       -h     Help; print version and usage info.

SEE ALSO

       afetch(1), alistat(1), compalign(1), compstruct(1), seqsplit(1), seqstat(1), sfetch(1), shuffle(1), sindex(1), sreformat(1), stranslate(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						REVCOMP(1)

STRANSLATE(1)						      General Commands Manual						     STRANSLATE(1)

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)