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.
LONG-ORFS(1)