Question: Is BLAST using Needleman-Wunsch or Smith-Waterman when aliging in between HSSPs?
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gravatar for Arjen Ten Have
5.9 years ago by
Mar del Plata Argentina
Arjen Ten Have350 wrote:

I am going thru my lectures for next month postgrad course and ran into a doubt. To me it would make sense to apply Needleman-Wunsch (Global) when aligning the subsequences in between the HSSPs identified in the earlier steps. But my class (which I made a couple of years ago) actually states it uses a "Smith-Waterman-like algorithm". Cannot find this in NCBIs handbook, Anybody any idea?

blast • 4.0k views
ADD COMMENTlink modified 3.7 years ago by mfilipav0 • written 5.9 years ago by Arjen Ten Have350
0
gravatar for Alex Reynolds
5.9 years ago by
Alex Reynolds31k
Seattle, WA USA
Alex Reynolds31k wrote:

A thorough walkthrough of the statistical method for an early version of BLAST can be found on pg. 345 of Ewens and Grant's Statistical Methods in Bioinformatics. Might be worth investigating.

ADD COMMENTlink modified 5.9 years ago • written 5.9 years ago by Alex Reynolds31k
0
gravatar for mfilipav
3.7 years ago by
mfilipav0
mfilipav0 wrote:

BLAST uses a local alignment algorithm, namely, Smith-Waterman.

ADD COMMENTlink written 3.7 years ago by mfilipav0

That seems a little broad/inaccurate. Would you happen to have a link to any documentation that suggests BLAST uses an algorithm as simple as SW?

ADD REPLYlink written 3.7 years ago by _r_am31k

Are you sure? I understood bLast is local since it is based on perfect, hence local matches that are extended to HSSPs that then become connected by a NW. It doesn't make sense to use SW since alignment between the HSSPs is from 0,0 to n,m where 0,0 corresponds with the first position following HSSPn and n,m is the position prior to HSSPn+1.

ADD REPLYlink written 3.7 years ago by Arjen Ten Have350
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