Ecosyste.ms: Awesome
An open API service indexing awesome lists of open source software.
https://github.com/naturale0/motifoccur
calculates probability of k-mer motif occurrence in n ntd random sequence
https://github.com/naturale0/motifoccur
bioinformatics sequence-motif
Last synced: 6 days ago
JSON representation
calculates probability of k-mer motif occurrence in n ntd random sequence
- Host: GitHub
- URL: https://github.com/naturale0/motifoccur
- Owner: naturale0
- Created: 2018-10-24T15:29:00.000Z (about 6 years ago)
- Default Branch: master
- Last Pushed: 2018-10-24T15:45:14.000Z (about 6 years ago)
- Last Synced: 2024-11-08T03:44:08.345Z (about 2 months ago)
- Topics: bioinformatics, sequence-motif
- Language: Python
- Homepage:
- Size: 34.2 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
This program computes probability of k-mer sequence motif occurence in n ntd random target sequence. There's [a blog post](https://de-novo.org/2018/10/25/sequence-motif-occurrence/) describing the rationale behind it. Python 3 needs to be installed.
## Manual
```
-h, --help show help message and exit
-k K [K ...] length of query sequence (k >= 3)
-n N [N ...] length of random target sequence
-p {0,1}, --plot {0,1}
Wheter or not to produce a plot
(0: no plot / 1: plot)
```
## examples
### 1. single input
```
./main -n 52 -k 7 -p 0
```
`n=52, k=7: 0.002804712821387148`
### 2. multiple inputs
```
./main -n 500 500 500 -k 3 4 7 -p 1
```
