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.
