Question on alignment

Question

[freezedry]

Hello all. Suppose we have 2 sequences. Sequence A and a longer sequence B.

How does one go about finding a segment of B such that the score of aligning the entire A and that segment is maximized?

I was thinking along the lines of the longest common subsequence. But i think it is incorrect. Since finding the subsequence might lead to the addition of gaps which lowers the score.

Thank you all for your time.

[Michael]

Using local alignment as your title suggests.

[freezedry]

Thanks for your suggestion. Hmm.. I think using local alignment might not work as the entire sequence A might not be aligned though.

[Devon Ryan]

It doesn't need to be, local alignment doesn't require that the entirety of either of the sequences are used.

[Michael]

Not sure what you are asking honestly. You are asking how to do an alignment? Isn't the answer obviously 'using an alignment algorithm'. Which one exactly to be further specified, just one of

global, global-local, local-global or local?

[GenoMax]

Have you looked at dot plots?

Answer 1

[matted]

It sounds like you want semi-global alignment (also known as "glocal"). You have to align all of A against a portion of B, so global isn't right (all of A against all of B) and local isn't right (some of A against some of B).

The algorithm is a hybrid of global and local alignment, as you might expect. See these lecture notes for more (somewhat randomly selected, but they look pretty good):

• Lecture notes 1
• Lecture notes 2