https://github.com/clemsciences/sequence_alignment
Sequence alignment algorithms
https://github.com/clemsciences/sequence_alignment
alignment sequence-alignment
Last synced: 11 months ago
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Sequence alignment algorithms
- Host: GitHub
- URL: https://github.com/clemsciences/sequence_alignment
- Owner: clemsciences
- License: mit
- Created: 2018-03-12T22:49:22.000Z (about 8 years ago)
- Default Branch: master
- Last Pushed: 2022-06-06T20:03:48.000Z (almost 4 years ago)
- Last Synced: 2025-02-17T09:43:47.016Z (about 1 year ago)
- Topics: alignment, sequence-alignment
- Language: Python
- Homepage:
- Size: 47.9 KB
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# Sequence alignment
[deterministic_alignment.py](https://github.com/clemsciences/sequence_alignment/blob/master/deterministic_alignment.py)
- Needleman-Wunsch algorithm: global alignment
- Smith-Waterman algorithm: local alignment
- Levenshtein distance: minimum number of operations (insertion, deletion, modification) to transform one sequence to an other sequence
[phmm.py](https://github.com/clemsciences/sequence_alignment/blob/master/phmm.py) : Pair Hidden Markov Model implementation
[blast.py](https://github.com/clemsciences/sequence_alignment/blob/master/blast.py) : heuristics to find local alignments in very long chains
[main.py](https://github.com/clemsciences/sequence_alignment/blob/master/main.py) : examples of presented algorithms
[data_retrieval.py](https://github.com/clemsciences/sequence_alignment/blob/master/data_retrieval.py) : word retrieval thanks to nltk
1. Install nltk with # apt-get install nltk
2. Download Swadesh corpus with
```python
>>> import nltk
>>> nltk.download()
```
[utils.py](https://github.com/clemsciences/sequence_alignment/blob/master/utils.py) : some useful functions which are unclassified
TODO: learning to align pairs of sequences with a Pair Hidden Markov Model.