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.