Awesome

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 (2002) by Lee, Grasso, and Sharlow and Generating consensus sequences from partial order ... (2003) by Lee

for education/demonstration purposes. A short description of the method can be found on this article 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 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.