[BiO BB] How to calculate the value of K and Lambda for two sequence alignment
golharam at umdnj.edu
Sat Feb 11 01:21:26 EST 2006
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.
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
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
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