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<DIV><SPAN class=044012006-11022006><FONT face=Arial color=#0000ff size=2>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.</FONT></SPAN></DIV>
<DIV><SPAN class=044012006-11022006><FONT face=Arial color=#0000ff
size=2></FONT></SPAN> </DIV>
<DIV><SPAN class=044012006-11022006><FONT face=Arial color=#0000ff
size=2>Ryan</FONT></SPAN></DIV>
<DIV><SPAN class=044012006-11022006><FONT face=Arial color=#0000ff
size=2></FONT></SPAN> </DIV>
<BLOCKQUOTE dir=ltr style="MARGIN-RIGHT: 0px">
<DIV></DIV>
<DIV class=OutlookMessageHeader lang=en-us dir=ltr align=left><FONT
face=Tahoma size=2>-----Original Message-----<BR><B>From:</B>
bio_bulletin_board-bounces+golharam=umdnj.edu@bioinformatics.org
[mailto:bio_bulletin_board-bounces+golharam=umdnj.edu@bioinformatics.org]
<B>On Behalf Of </B>shohag md<BR><B>Sent:</B> Friday, February 03, 2006 6:26
AM<BR><B>To:</B> bio_bulletin_board@bioinformatics.org<BR><B>Subject:</B> [BiO
BB] How to calculate the value of K and Lambda for two sequence
alignment<BR><BR></FONT></DIV>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT face="Times New Roman">Hi
Everybody</FONT></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT
face="Times New Roman"></FONT> </P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT
face="Times New Roman">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 </FONT></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT
face="Times New Roman"></FONT> </P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT face="Times New Roman">E
= Kmn e <SUP>-</SUP></FONT><SUP><SPAN
style="FONT-FAMILY: Symbol; mso-ascii-font-family: 'Times New Roman'; mso-hansi-font-family: 'Times New Roman'; mso-char-type: symbol; mso-symbol-font-family: Symbol">
<SPAN
style="mso-char-type: symbol; mso-symbol-font-family: Symbol">l</SPAN></SPAN><FONT
face="Times New Roman">x</FONT></SUP></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SUP><FONT
face="Times New Roman"><SPAN
style="mso-spacerun: yes"></SPAN></FONT></SUP> </P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT
face="Times New Roman">But how can I calculate the value of K and </FONT><SPAN
style="FONT-FAMILY: Symbol; mso-ascii-font-family: 'Times New Roman'; mso-hansi-font-family: 'Times New Roman'; mso-char-type: symbol; mso-symbol-font-family: Symbol"><SPAN
style="mso-char-type: symbol; mso-symbol-font-family: Symbol">l</SPAN></SPAN><FONT
face="Times New Roman"> .</FONT></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT
face="Times New Roman"></FONT> </P>
<DIV><SPAN
style="FONT-SIZE: 12pt; FONT-FAMILY: 'Times New Roman'; mso-fareast-font-family: 'Times New Roman'; mso-ansi-language: EN-US; mso-fareast-language: EN-US; mso-bidi-language: AR-SA">Is
there any formula that can help me to calculate the value of K and
</SPAN><SPAN
style="FONT-SIZE: 12pt; FONT-FAMILY: Symbol; mso-ascii-font-family: 'Times New Roman'; mso-hansi-font-family: 'Times New Roman'; mso-char-type: symbol; mso-symbol-font-family: Symbol; mso-fareast-font-family: 'Times New Roman'; mso-ansi-language: EN-US; mso-fareast-language: EN-US; mso-bidi-language: AR-SA; mso-bidi-font-family: 'Times New Roman'"><SPAN
style="mso-char-type: symbol; mso-symbol-font-family: Symbol">l</SPAN></SPAN><SPAN
style="FONT-SIZE: 12pt; FONT-FAMILY: 'Times New Roman'; mso-fareast-font-family: 'Times New Roman'; mso-ansi-language: EN-US; mso-fareast-language: EN-US; mso-bidi-language: AR-SA">
,<SUP> <SPAN style="mso-spacerun: yes"> </SPAN></SUP>and then the
expectation value.</SPAN></DIV>
<DIV><SPAN
style="FONT-SIZE: 12pt; FONT-FAMILY: 'Times New Roman'; mso-fareast-font-family: 'Times New Roman'; mso-ansi-language: EN-US; mso-fareast-language: EN-US; mso-bidi-language: AR-SA"></SPAN> </DIV>
<DIV><SPAN
style="FONT-SIZE: 12pt; FONT-FAMILY: 'Times New Roman'; mso-fareast-font-family: 'Times New Roman'; mso-ansi-language: EN-US; mso-fareast-language: EN-US; mso-bidi-language: AR-SA">Thanking
all in advance<BR><BR>Shoyaib<BR></SPAN></DIV></BLOCKQUOTE></BODY></HTML>