Question

BLAST vs Smith-Waterman

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2.5 years ago

pedro.lopez14 ▴ 10

Can BLAST and Smith-Waterman return the same alignment?

Alignment BLAST Smith-Waterman • 1.4k views

ADD COMMENT • link updated 2.5 years ago by lieven.sterck 15k • written 2.5 years ago by pedro.lopez14 ▴ 10

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on top of what Mensur Dlakic already posted below: SW is an alignment tool, BLAST is a search tool making use of alignments (== the "google" for sequences), so their goals are somewhat different ...

SW wants to output the best alignment between two sequences, BLAST wants to output as fast as possible similar sequences to your query.

ADD REPLY • link 2.5 years ago by lieven.sterck 15k

score 2 · Answer 1 · 2022-04-22

As both are local alignment algorithms, the answer is yes. However, there is no guarantee that will be the case. BLAST takes some shortcuts in creating seed alignments and high-scoring pairs, which makes it quite a bit faster than SW. SW alignments are locally optimal and will in some cases be different from BLAST, and sometimes of higher quality. These are often marginal cases, and not scoring and aligning some sequences properly is usually worth it given the BLAST speed advantage over SW.

There is a longer explanation:

https://people.montefiore.uliege.be/kvansteen/GBIO0009-1/ac20092010/Class4/BE-smith-waterman_versus_blast.pdf

Some of the comparisons may not be valid now as this article is 15 years old, but the main message about pros and cons still holds.