[BiO BB] How to calculate the value of K and Lambda for two sequence alignment

[Ryan Golhar]

Did anyone ever respond to you on this?  K and lambda.  I forget where K
comes from.  Lambda is dependent on the scoring matrix you are using.  I
believe it is given with the matrix.  BLOSUM uses 0.347.
 
Ryan
 

-----Original Message-----
From: bio_bulletin_board-bounces+golharam=umdnj.edu at bioinformatics.org
[mailto:bio_bulletin_board-bounces+golharam=umdnj.edu at bioinformatics.org
] On Behalf Of shohag md
Sent: Friday, February 03, 2006 6:26 AM
To: bio_bulletin_board at bioinformatics.org
Subject: [BiO BB] How to calculate the value of K and Lambda for two
sequence alignment



Hi Everybody

 

Using Smith Waterman algorithm I want to align two sequences. Aftet that
I want to calculate the expectation value. For calculating the
expectation value we know that 

 

E = Kmn e - lx

 

But how can I calculate the value of K and l .

 

Is there any formula that can help me to calculate the value of K and l
,  and then the expectation value.
 
Thanking all in advance

Shoyaib


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