This is the command tigr-extract that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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.
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