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)