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

# tigr-long-orfs(1)

Find/Score potential genes in genome-file using the probability model in icm-file

## NAME

long-orfs — Find/Score potential genes in genome-file using  the probability model in icm-file

## SYNOPSIS

**tigr-long-orgs** \[genome-file *options\]*

## DESCRIPTION

*Program long-orfs takes a sequence file (in FASTA format) and*  *outputs a list of all long "potential genes" in it that do not*  *overlap by too much.  By "potential gene" I mean the portion of*  *an orf from the first start codon to the stop codon at the end.*

*The first few lines of output specify the settings of various*  *parameters in the program:*

*Minimum gene length is the length of the smallest fragment*  *considered to be a gene.  The length is measured from the first base*  *of the start codon to the last base \*before\* the stop codon.*  *This value can be specified when running the program with the  -g  option.*  *By default, the program now (April 2003) will compute an optimal length*  *for this parameter, where "optimal" is the value that produces the*  *greatest number of long ORFs, thereby increasing the amount of data*  *used for training.*

*Minimum overlap length is a lower bound on the number of bases overlap*  *between 2 genes that is considered a problem.  Overlaps shorter than*  *this are ignored.*

*Minimum overlap percent is another lower bound on the number of bases*  *overlap that is considered a problem.  Overlaps shorter than this*  *percentage of \*both\* genes are ignored.*

*The next portion of the output is a list of potential genes:*

*Column 1 is an ID number for reference purposes.  It is assigned*  *sequentially starting with  1  to all long potential genes.  If*  *overlapping genes are eliminated, gaps in the numbers will occur.*  *The ID prefix is specified in the constant  ID\_PREFIX .*

*Column 2 is the position of the first base of the first start codon in*  *the orf.  Currently I use atg, and gtg as start codons.  This is*  *easily changed in the function  Is\_Start () .*

*Column 3 is the position of the last base \*before\* the stop codon.  Stop*  *codons are taa, tag, and tga.  Note that for orfs in the reverse*  *reading frames have their start position higher than the end position.*  *The order in which orfs are listed is in increasing order by*  *Max {OrfStart, End}, i.e., the highest numbered position in the orf,*  *except for orfs that "wrap around" the end of the sequence.*

*When two genes with ID numbers overlap by at least a sufficient*  *amount (as determined by Min\_Olap and Min\_Olap\_Percent ), they*  *are eliminated and do not appear in the output.*

*The final output of the program (sent to the standard error file so*  *it does not show up when output is redirected to a file) is the*  *length of the longest orf found.*

*Specifying Different Start and Stop Codons:*

*To specify different sets of start and stop codons, modify the file*  *gene.h .  Specifically, the functions:*

*Is\_Forward\_Start     Is\_Reverse\_Start     Is\_Start*  *Is\_Forward\_Stop      Is\_Reverse\_Stop      Is\_Stop*

*are used to determine what is used for start and stop codons.*

*Is\_Start  and  Is\_Stop  do simple string comparisons to specify*  *which patterns are used.  To add a new pattern, just add the comparison*  *for it.  To remove a pattern, comment out or delete the comparison*  *for it.*

*The other four functions use a bit comparison to determine start and*  *stop patterns.  They represent a codon as a 12-bit pattern, with 4 bits*  *for each base, one bit for each possible value of the bases, T, G, C*  *or A.  Thus the bit pattern  0010 0101 1100  represents the base*  *pattern  \[C\] \[A or G\] \[G or T\].  By doing bit operations (& \| ~) and*  *comparisons, more complicated patterns involving ambiguous reads*  *can be tested efficiently.  Simple patterns can be tested as in*  *the current code.*

*For example, to insert an additional start codon of CAT requires 3 changes:*  *1. The line*  *\|\| (Codon & 0x218) == Codon*  *should be inserted into  Is\_Forward\_Start , since 0x218 = 0010 0001 1000*  *represents CAT.*  *2. The line*  *\|\| (Codon & 0x184) == Codon*  *should be inserted into  Is\_Reverse\_Start , since 0x184 = 0001 1000 0100*  *represents ATG, which is the reverse-complement of CAT.  Alternately,*  *the #define constant  ATG\_MASK  could be used.*  *3. The line*  *\|\| strncmp (S, "cat", 3) == 0*  *should be inserted into  Is\_Start .*

## OPTIONS

- **-g** *n*

  *Set minimum gene length to n.  Default is to compute an*  *optimal value automatically.  Don't change this unless you*  *know what you're doing.*

- **-l**

  *Regard the genome as linear (not circular), i.e., do not allow*  *genes to "wrap around" the end of the genome.*  *This option works on both  glimmer and long-orfs .*  *The default behavior is to regard the genome as circular.*

- **-o** *n*

  *Set maximum overlap length to n.  Overlaps shorter than this*  *are permitted.  (Default is 0 bp.)*

- **-p** *n*

  *Set maximum overlap percentage to n%.  Overlaps shorter than*  *this percentage of \*both\* strings are ignored.  (Default is 10%.)*

## SEE ALSO

*tigr-glimmer3 (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.*