tigr-glimmer(1) [debian man page]

TIGR-GLIMMER(1) 					      General Commands Manual						   TIGR-GLIMMER(1)

NAME

       tigr-glimmer - runs various programs of the TIGR Glimmer suite

SYNOPSIS

       tigr-glimmer program [arguments]

DESCRIPTION

       This  manual  page  documents  briefly  the tigr-glimmer wrapper to the TIGR Glimmer programs.  This manual page was written for the Debian
       GNU/Linux distribution because upstream does not provide this wrapper and it was invented for Debian to avoid conflicts with other packages
       that might cause a name space polution.

       tigr-glimmer is just a wrapper that invokes the various programs in the TIGR Glimmer software package. You can get more detailed documenta-
       tion in /usr/share/doc/tigr-glimmer.  Please note that the documentation there is a part of the former  version	Glimmer  2.   The  version
       Glimmer 3 has some features that were described in the notes.pdf document inside the documentation directory.

       The  following programs are included: anomaly, build-fixed, build-icm, entropy-profile, entropy-score, extract, glimmer3, long-orfs, multi-
       extract, score-fixed, start-codon-distrib, test, uncovered and window-acgt.

OPTIONS

       There are no options.

EXAMPLES

       tigr-glimmer build-icm

       tigr-glimmer long-orfs

SEE ALSO

       For the pre previously packaged version Glimmer2 some text files from the documentation were turned to man pages for the  Debian  GNU/Linux
       distribution by Steffen Moeller <moeller@debian.org>

AUTHORS

       This manual page was written by Andreas Tille <tille@debian.org>, for the Debian GNU/Linux system (but may be used by others).

								  April 16, 2008						   TIGR-GLIMMER(1)

TIGR-GLIMMER(1) 					      General Commands Manual						   TIGR-GLIMMER(1)

NAME

       tigr-glimmer -- Fine start/stop positions of genes in genome sequence

SYNOPSIS

       tigr-extract [genome-file options]

DESCRIPTION

       Program	extract  takes a FASTA format sequence file and a file with a list of start/stop positions in that file  (e.g., as produced by the
       long-orfs  program) and extracts and outputs the specified sequences.

       The first command-line argument is the name of the sequence file, which must be in FASTA format.

       The second command-line argument is the name of the coordinate file.  It must contain a list of pairs of positions in the first	file,  one
       per line.  The format of each entry is:

       <IDstring>>  <start position>  <stop position>

       This  file  should  contain  no other information, so if you're using the output of  glimmer  or  long-orfs , you'll have to cut off header
       lines.

       The output of the program goes to the standard output and has one line for each line in	the  coordinate  file.	 Each  line  contains  the
       IDstring  ,  followed  by  white space, followed by the substring of the sequence file specified by the coordinate pair.  Specifically, the
       substring starts at the first position of the pair and ends at the second position (inclusive).	If the first position is bigger  than  the
       second,	then  the  DNA	reverse  complement  of each position is generated.  Start/stop pairs that "wrap around" the end of the genome are
       allowed.

OPTIONS

       -skip	 makes the output omit the first 3 characters of each sequence, i.e., it skips over the start codon.  This was	the  behaviour	of
		 the previous version of the program.

       -l	 makes	the  output  omit an sequences shorter than  n	characters.  n	includes the 3 skipped characters if the  -skip  switch is
		 one.

SEE ALSO

       tigr-glimmer3 (1), tigr-long-orfs (1), tigr-adjust (1), tigr-anomaly   (1), tigr-build-icm (1), tigr-check (1), tigr-codon-usage (1), tigr-
       compare-lists (1), tigr-extract (1), tigr-generate (1), tigr-get-len (1), tigr-get-putative (1),

       http://www.tigr.org/software/glimmer/

       Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer3.

AUTHOR

       This manual page was quickly copied from the glimmer web site by Steffen Moeller moeller@debian.org for the Debian system.

																   TIGR-GLIMMER(1)