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)