The Changing Faces of Sequence Alignment: Fitting Alignment
Explore the fitting alignment technique to compare biological sequences when global or local alignment methods are inadequate. Understand how to find the best substring match that maximizes alignment scores between a longer protein sequence and a shorter one, improving accuracy for bioinformatics analysis.
We'll cover the following...
Maximizing the global alignment score
Say that we wish to compare the approximately 20,000 amino acid-long NRP synthetase
from Bacillus brevis with the approximately 600 amino acid-long A-domain from Streptomyces roseosporus, the bacterium that produces the powerful antibiotic Daptomycin. We
hope to find a region within the longer protein sequence v that has high similarity with
all of the shorter sequence w. Global alignment will not work because it tries to align all
of v to all of w; local alignment will not work because it tries to align substrings of both
v and w. Thus, we have a distinct alignment application called the Fitting Alignment
Problem.
“Fitting” w to v requires finding a substring ...