Question: Global alignment with one sequence larger than another
0
gravatar for Gustavo Temple
23 days ago by
Gustavo Temple0 wrote:

If a sequence α is much larger than β, then is there an optimal global alignment between α and β that does not add gaps in α? Considering an alignment scoring scheme such that gap ≤ mismatch < 0 < match.

alignment • 134 views
ADD COMMENTlink modified 22 days ago by RamRS18k • written 23 days ago by Gustavo Temple0
2

Yes, if β is identical to a small, contiguous region of α, the optimal alignment would have no gaps. However, when aligning two sequence of very disparate sizes, the heuristics used to speed up the algorithms could return a sub-optimal alignment, instead of the optimal.

ADD REPLYlink written 21 days ago by h.mon20k

Is this an assignment question?

ADD REPLYlink written 23 days ago by WouterDeCoster32k

No, it is a conceptual doubt (I am a beginner).

ADD REPLYlink written 23 days ago by Gustavo Temple0

Is the statement taken from a book? It looks too ... framed

ADD REPLYlink written 23 days ago by RamRS18k
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