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资源说明：Optimal and non overlapping DNA repeat searcher
# Agate
**An optimal and non-overlapping DNA repeat searcher.**
Includes tools for dealing poly-purine/poly-pyrimidine tracts (PPTs).
## What does that mean?
What it means is that `agate` will search of repeats in DNA sequences, but
unlike most repeat finder tools, it will only return the best matches and any
sequence segment can only be associated with one reported repeat.
## Why?
There is a bunch of extra work in trying to select the optimal sequence and
allow for mismatch errors. Most repeat finders show you a whole bunch of
candidate matches, and sometimes you just want the best. The selection of these
can in turn impact the selection of neighbouring repeat sequences etc.
For the particular research problem that the software was created
to address, no overlaps was a condition.
## The tools
This repo contains source for four executables. They are probably not master
pieces of software engineering as I wrote them in my free time while doing
a PhD in an unrelated area, and the requirements changes substantially while
developing each tool:
- **repeat-finder**: Main program for finding optimal and exclusive repeating
motifs using mismatches. Further description found below.
- **ppt-se**: Looks for poly-purine/poly-pyrimidine tracts (PPTs) with an
internal axis of symmetry. This includes, for example, AAAGAAA, GAGGAG. It
has the additional commands "sel" and "seu" which specify the size limits of
the symmetrical element.
- **ppt-mismatch**: Has the additional capability of finding PPT arrays with
mismatches, the "e" command specified the block size within which only one
mismatch is allowed. Mismatches are also disallowed within the terminal two
nucleotides.
- **ppt**: Looks for PPTs eg AAAAAAAA, AGGGGA, GGGGG, CCCCCC, CCTCTTTCC,
TTTTTT. "l" and "u" are size limiters for the overall tract size.
- **expected**: Calculates the expected number of repeats based on the
equations in the paper: _de Wachter, Rupert (1981). The Number of Repeats
Expected in Random Nucleic Acid Sequences and Found in Genes. J. theor.
Biol. 91, 71-98_
## Dependencies
RepeatFinder has been developed in C with a minimal of dependencies.
It should be compilable on any operating environment that supports
the standard ANSI C library.
By default the compilation system is setup to support the Make build
system supported by the GCC compiler
## Compilation
Simply typing make in the source directory should compile three executables:
agate-repeat-finder, ppt, ppt-mismatch, ppt-se, expected
If you don't have the Make build system you will have to compile and link the
source code yourself. You may need to check the Makefile environment variables
to see that they conform to your setup.
## Instructions for use
### Create a database of matches.
This is done with the "-d" option followed by a number indicating the maximum
size of motifs to look for. e.g.
$ repeat-finder.exe -d 3 chr01.fsa
This will look for motifs of size 3 and below in the file "chr01.fsa".
This is the most time consuming part and once you have run it you shouldn't
have to run it again unless you want to change the maximum size of motifs or
you get a new version of the program. The database filename is the same as the
sequence with ".database" appended. So for the above example, a database file
called "chr01.fsa.database" is created.
The database file *must* be the same as the sequence filename with ".database"
appended. So if you rename the sequence file, you must rename the database file
or regenerate it.
#### Changing the error distance.
By default databases are created with a minimum error distance of 5. If you
wish to alter this you can also specify an error distance when you create
a database using the "-e" option. e.g.
$ repeat-finder.exe -d 3 -e 7 chr01.fsa
Sets the minimum error distance to be 7 nucleotides.
### Normal matching
Specify what matches you are interested in using the following:
```
-f - Output the flanking bases
to a match (default 50)
-n - search for motifs of size .
You can use this option more than once, for example to
specify motifs of sizes 1 and 2 you can use "-n 2 -n 1"
-m - search for a particular motif.
e.g "-m ATT". You can also use this more than once.
-l - find matches with at least repeats.
-u - ignore matches with more than repeats.
-lp - lowest purity repeats to find
-up - greatest purity repeats to find
(Note: range of purities is constrained by error distance)
```
Results are output to the file "results.csv". Be warned that this is
overwritten if it already exists so rename results you wish to keep.
### Compound Repeats
Use "-cr" to look for compound repeats, and "-gap" to specify the maximum gap
between repeats. If you only are interested in degenerate repeats then use
"-dr" as "-cr" looks for both compound and degenerate repeats.
You also must use the options for normal matches to specify which ones to
output. e.g.
$ repeat-finder -cr -gap 4 -n 2 chr01.fsa
Looks for compound repeats with a gap of at most 4. It then filters these for
only those that have at least one sub-repeat with a motif of size 2.
Results are output to the file "results.csv". The compound matches are reported
at the end, and also has a column to indicate the the indexes of the sub
repeats.
### Extracting to FASTA
To output to a fasta file use "-i" option along with the index of the match. If
the index is of a compound repeat you must also specify either -cr or -dr
(depending on what you used to get the index) and the same -gap number on the
command line.
You can use the index "-1" to indicate that all repeats should be output to
fasta.
The file created is by default called "repeats.fsa"
## What research has this been used in?
- **Bagshaw, A., Pitt, J.P.W., Gemmell, N.J.** (2008). High frequency of
microsatellites in S. cerevisiae meiotic recombination hotspots. _BMC
Genomics_ 9:49 doi:10.1186/1471-2164-9-49
- **Bagshaw, A., Pitt, J.P.W., Gemmell, N.J.** (2006). Association of
poly-purine/poly-pyrimidine sequences with meiotic recombination hot spots.
_BMC Genomics_ 7:179, doi:10.1186/1471-2164-7-179
And I've heard it's been used by a few other people in the same lab, although
perhaps not to a sufficient extent to be referenced.
## Availability
Code repository on github: https://github.com/ferrouswheel/agate
## The name
NOTE: This project used to be called repeatfinder and be [hosted on
sourceforge](http://repeatfinder.sf.net), but then they broke the drupal website
and I'm more fond of github. The reason for the name change is that there are
many other pieces of software called "repeatfinder" that do the same thing.
"Agate" is a [satellite/missle name](http://planet4589.org/space/misc/names.html)
and was the shortest name mostly composed of nucleotide letters ;-)
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