https://github.com/linsalrob/repeatfinder
fast code for searching for direct and indirect repeats in DNA sequences.
https://github.com/linsalrob/repeatfinder
Last synced: over 1 year ago
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fast code for searching for direct and indirect repeats in DNA sequences.
- Host: GitHub
- URL: https://github.com/linsalrob/repeatfinder
- Owner: linsalrob
- License: mit
- Created: 2024-04-19T01:49:53.000Z (about 2 years ago)
- Default Branch: main
- Last Pushed: 2024-06-12T01:53:00.000Z (about 2 years ago)
- Last Synced: 2024-06-12T13:09:36.022Z (about 2 years ago)
- Language: Python
- Size: 102 KB
- Stars: 2
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
- Citation: citation.cff
Awesome Lists containing this project
README
[](https://edwards.sdsu.edu/research)
[](https://opensource.org/licenses/MIT)
[](https://zenodo.org/doi/10.5281/zenodo.11565325)
# Repeat Finder - Finding Repeats in DNA sequences
Repeatfinder is a stand alone program to quickly find repeats in DNA sequences. You might find that it is remarkably similar to an essential module in [PhiSpy](http://github.com/linsalrob/PhiSpy).
# How to find repeats
## Using the command line
You can use the `pydna_repeatfinder` command to find repeats in a fasta sequence.
By default, `pydna_repeatfinder` just prints the repeats in a `simple` tab-separated format that is easy to read and includes the DNA sequence.
For example:
```
$ pydna_repeatfinder -f tests/test_long.fasta
random_sequence Number:1 Len1:52 Len2:52 92 144 1946 1998 TCAGTTGTCGTAGGTTAGCCTAAGGGTATCGCGGAAGTATGGAGTATACGGT TCAGTTGTCGTAGGTTAGCCTAAGGGTATCGCGGAAGTATGGAGTATACGGT
random_sequence Number:2 Len1:52 Len2:52 92 144 197 145 TCAGTTGTCGTAGGTTAGCCTAAGGGTATCGCGGAAGTATGGAGTATACGGT CACCGTATACTCCATACTTCCGCGATACCCTTAGGCTAACCTACGACAACTG
random_sequence Number:3 Len1:53 Len2:53 145 198 1998 1945 CACCGTATACTCCATACTTCCGCGATACCCTTAGGCTAACCTACGACAACTGA ATCAGTTGTCGTAGGTTAGCCTAAGGGTATCGCGGAAGTATGGAGTATACGGT
```
There are two long repeats here. The first from 92-144 is repeated in the same orientation (a direct repeat) at position 1946-1998.
We can also output the results formated so you can paste them directly into a GenBank file. This is perhaps the easiest way to visualise the repeats.
```
$ pydna_repeatfinder -f tests/test_long.fasta -o genbank
repeat_region join(92..144,1946..1998)
/note="direct repeat number 1 of length 53"
/rpt_type="direct"
repeat_region join(92..144,complement(197..145))
/note="inverted repeat number 2 of length 53"
/rpt_type="inverted"
repeat_region join(145..198,complement(1998..1945))
/note="inverted repeat number 3 of length 54"
/rpt_type="inverted"
```
## In your own code
You can import the `pydna_repeatfinder` module and use it in your own code:
```
from PyRepeatFinder import find_repeats
r = find_repeats(dna_seq, gap_len, min_len, 0)
for rpt in r:
# rpt is a dictionary with keys:
# repeat_number
# first_start
# first_end
# second_start
# second_end
```
We are happy to add more output formats, please post a GitHub issue and tag it as an enhancement.
# Installing pydna_repeatfinder
You should install it using [bioconda](https://bioconda.github.io/):
```
mamba create -n pydna_repeatfinder -c bioconda pydna_repeatfinder
mamba activate pydna_repeatfinder
```
# Citing pydna_repeatfinder
Please see the citation file.