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https://github.com/ljdursi/poapy
A simple Partial Order Aligner based on Lee, Grasso and Sharlow (2002), for education/demonstration purposes
https://github.com/ljdursi/poapy
Last synced: 3 months ago
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A simple Partial Order Aligner based on Lee, Grasso and Sharlow (2002), for education/demonstration purposes
- Host: GitHub
- URL: https://github.com/ljdursi/poapy
- Owner: ljdursi
- License: gpl-3.0
- Created: 2015-04-28T21:38:45.000Z (over 9 years ago)
- Default Branch: master
- Last Pushed: 2024-06-20T14:00:09.000Z (5 months ago)
- Last Synced: 2024-06-22T05:29:05.930Z (5 months ago)
- Language: Python
- Size: 184 KB
- Stars: 70
- Watchers: 8
- Forks: 12
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
- Awesome-Bioinformatics - POA - Partial-Order Alignment for fast alignment and consensus of multiple homologous sequences. [ [paper-2002](https://academic.oup.com/bioinformatics/article/18/3/452/236691) ] (Next Generation Sequencing / Sequence Alignment)
README
# A Simple Partial Order Alignment implementation
This is a simple python implementation of a Partial Order Alignment for MSA,
based on
[Multiple sequence alignment using partial order graphs](http://bioinformatics.oxfordjournals.org/content/18/3/452.short) (2002) by Lee, Grasso, and Sharlow
and
[Generating consensus sequences from partial order ...](http://bioinformatics.oxfordjournals.org/content/19/8/999.short) (2003) by Lee
for education/demonstration purposes. A short description of the method can be found on [this article](http://simpsonlab.github.io/2015/05/01/understanding-poa/) on the SimpsonLab group blog.
Some examples are provided; they are run as
```
$ ./poa.py examples/example4.fa --html ex4.html
seq1 -------------------------------TGTACNTG-TTTGTG-AGG-CTA
seq2 ---AGTTCCTGCTGCG--TTTGCTGGACTGATGTACTTG-TTTGTG-AGG-CAA
seq3 ---AGTTCCTGCTGCG--TTTGCTGGACTTATGTACTTG-TTTGTG-AGG-CAA
seq4 --AAGTTCCTGCTGCG--TTTGCTGGACTGATGTACTTGGTTTGTGNAGG-CAA
seq5 ---AGTTCCTGCTGCG--TTTGCTGGACTGATGTACTTG-TTTGT-NAGG-CAA
seq6 ---AGTTCCTGCTGCG--TTTGCT------------------------------
seq7 ---AGTTCCTGCTGCG--TTTGCTGGACTGATGTACTTG-TTT-----------
seq8 ---AGTTCCTGCTGCG--TTTGCTGGACTGATGTACTTG-TTTGTG-AGG-CAA
seq9 ---AGTTNCTGNTGNG--TTTGCTGGACTGATGTACTTG-TTTGTG-AGG-CAA
seq10 --------------------------------GTACNTG-TTTGTG-AGG-CTA
seq11 ---AGTTCCTGCTGCG--TTTGCTGGACTGATGTACTTG-TTTGTG-AGG-CAA
seq12 ---AGTTCCTGCTGCG--TTTGCTGGACTGATGTACTTG-TTTGTG-AGG-CAA
seq13 ---AGTTCCTGCTGCG--TTTGCTGGACTGATGTACTTG-TTTGTG-AGG-CAA
seq14 ---AGTTCCTGCTGCT--TTTGCTGGACTGATGTACTTG-ATTGTG-AGG-CAA
seq15 ---AGTTCCTGCTGCG--TTTGCTGGACTGATGTACTTG-TTTGTG-AGG-CAA
seq16 ---AGTTCCTGCTGCG--CTTGCTGGACTGATGTACTTG-TTTGTG-AGG-CAA
seq17 ---AGTTCCTGCTGCG--TTTGCTGGACTGATGTACTTG-TTTGTG-CGG-CAA
seq18 ---AGT-CCTGC-GCG--TTTGC-GGACGGATGTACTTG--TTGTG-AGG-CAA
seq19 -------------------------------------------------G-CAA
seq20 ------------------------------------------------GG-CAA
seq21 ---------------------------CTGATGTACTTG--TTGTG-AGGGCAA
seq22 ---AGTTCCTGCTGCG--TTTGCTGGACTGATGTACTTG-TTTGTG-AGG-CAA
seq23 -G----TTCTGCCTGC-GTTTGCTGAACTGATGTACTTG-TTAGT--AAG-CAA
seq24 C---GTTACTGC-GGGG-TTTGCTGGACTCATG-ACTTTGTTNGTA-G-G-CAA
Consensus0 --AAGTTCCTGCTGCG--TTTGCTGGACTGATGTACTTG-TTTGTG-AGG-CAA
```
which produces an HTML file ex4.html, which uses [viz.js](http://visjs.org/)
to give an interactive output of small alignments; the output from above looks
like:
**NOTE**: This version has been modified from the earlier version to remove
affine gap penalties (which I hadn't originally been doing correctly!).
The correct affine gap calculation introduces enough complication to somewhat
obscure the important part of this example code, which is the graph-string
alignment, so what remains is a simple linear gap model.