Multiple Sequence Alignment with Custom ClustalW Implementation

University Projects #Data Science#Python#Bioinformatics

Overview#

A custom implementation of the ClustalW multiple sequence alignment algorithm using dynamic programming. The system progressively aligns biological sequences by building scoring matrices and tracing back optimal alignments. You can view the code here.

Key Achievements#

Successfully aligned 4 sequences (GTTAT, CGTTT, GCAAT, CCGAT) through progressive alignment
Identified and resolved a complex infinite loop bug through systematic debugging
Produced correct alignments matching expected ClustalW output

Results#

Aligning A (GTTAT) with B (CGTTT)#

Aligning C (GCAAT) with D (CCGAT)#

Aligning AB with CD#

Implementation#

Algorithm Process#

Build dynamic programming table with first row/col set up
Fill table with max score for each cell using Sum-of-Pairs
Find optimal alignment by tracing back through from end to start
Align aligned sequences together progressively

Debugging#

The initial implementation had a critical bug causing infinite loops during traceback on the AB-CD alignment phase. I systematically identified and fixed the issues:

Bug	Fix
Infinite loop in traceback	`while True` to `while row>=0 and col>=0`
Progress not made in all branches	Update scores in all conditional branches
Exit check missing	Add end of table boundary check
Alignment tracking issue	Optimal alignment array
Scoring inconsistency	Ensure fillTable and traceback use scores the same