---
name: "tigr-extract"
section: "1"
platform: "linux"
package: "tigr-glimmer"
version: "3.02b-6+b1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/tigr-extract"
---

# tigr-extract(1)

Fine start/stop positions of genes in genome sequence

## 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.*