Thread Subject: doubt "nwalign" function

Subject: doubt "nwalign" function

From: Arthur Zheng

Date: 11 Oct, 2008 19:26:02

Message: 1 of 1

I am using the "nwalign" function of matlab R2007a to do global alignment. I use the example on P21 from the book Biological sequence analysis bu R. Durbin.
Below is my code:
****************************************************
A = 'HEAGAWGHEE';
B = 'PAWHEAE';
ScoringMatrixValue = 'BLOSUM50';

[Score, Alignment] = nwalign(A, B, 'Alphabet', 'AA', 'ScoringMatrix', ScoringMatrixValue,'GapOpen', 8, 'ExtendGap', 8,'Showscore', true);
****************************************************
The result is:
Score = 0.3333

Alignment =
HEAGAWGHE-E
    || || |
--P-AW-HEAE

My question is the Alignment is right (the same as in the book), but why the Score is 0.3333? You can easily calculate the alignment score,which should be 1 as shown in the book.

Is there something wrong with the function "nwalign"??

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Tag Activity for This Thread
Tag Applied By Date/Time
nwalign Arthur Zheng 11 Oct, 2008 15:30:08
sequence alignment Arthur Zheng 11 Oct, 2008 15:30:08
bioinformatics Arthur Zheng 11 Oct, 2008 15:30:08
global alignment Arthur Zheng 11 Oct, 2008 15:30:08
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