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)