<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<HTML><HEAD>
<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=us-ascii">
<TITLE>Message</TITLE>
<META content="MSHTML 6.00.2800.1528" name=GENERATOR></HEAD>
<BODY>
<BLOCKQUOTE style="MARGIN-RIGHT: 0px">
<DIV></DIV>
<DIV class=OutlookMessageHeader lang=en-us dir=ltr align=left><FONT
face=Tahoma><FONT size=2><SPAN class=624274817-11042006><FONT face=Arial
color=#0000ff>Do you think a percent identity comparison be
useful? In other words, how often does matrix A give a higher
percent identity than matrix B?</FONT></SPAN></FONT></FONT></DIV>
<DIV class=OutlookMessageHeader lang=en-us dir=ltr align=left><FONT
face=Tahoma><FONT size=2><SPAN
class=624274817-11042006></SPAN></FONT></FONT> </DIV>
<DIV class=OutlookMessageHeader lang=en-us dir=ltr align=left><FONT
face=Tahoma><FONT size=2><SPAN
class=624274817-11042006> </SPAN></FONT></FONT></DIV>
<DIV class=OutlookMessageHeader lang=en-us dir=ltr align=left><FONT
face=Tahoma><FONT size=2><SPAN
class=624274817-11042006></SPAN></FONT></FONT> </DIV>
<DIV class=OutlookMessageHeader lang=en-us dir=ltr align=left><FONT
face=Tahoma><FONT size=2><SPAN
class=624274817-11042006> </SPAN>-----Original
Message-----<BR><B>From:</B> Martin Gollery [mailto:marty.gollery@gmail.com]
<BR><B>Sent:</B> Tuesday, April 11, 2006 1:41 PM<BR><B>To:</B>
golharam@umdnj.edu; The general forum at Bioinformatics.Org<BR><B>Subject:</B>
Re: [BiO BB] Theoretical Scoring Matrix Question<BR><BR></DIV></FONT></FONT>Hi
Ryan,<BR><BR>Pick a number of sequence pairings, some where you know that the
sequences are related and some where you know that they are not related. Your
matrices should hopefully provide better discrimination than ednafull or
BLAST, that is, they should provide more positive scores for the true
positives and more negative scores for the known negatives. You need to do
this on a large number of sequences to get a good picture- one or two is not
enough. <BR><BR>Best,<BR>Marty<BR><BR><BR>
<DIV><SPAN class=gmail_quote>On 4/11/06, <B class=gmail_sendername>Ryan
Golhar</B> <<A onclick="return top.js.OpenExtLink(window,event,this)"
href="mailto:golharam@umdnj.edu" target=_blank>golharam@umdnj.edu</A>>
wrote:</SPAN>
<BLOCKQUOTE class=gmail_quote
style="PADDING-LEFT: 1ex; MARGIN: 0pt 0pt 0pt 0.8ex; BORDER-LEFT: rgb(204,204,204) 1px solid">I've
constructed a few scoring matrices for DNA sequence based on<BR>certain
information. I'm now trying to determine how well they
perform<BR>compared to the standard statistically based matrices, such as
EDNAFULL<BR>(+5/-4) and the standard scoring matrix used by BLAST (+1/-3).
<BR><BR>My question is, what would be a valid test to compare matrices
against<BR>each
other?<BR><BR>Ryan<BR><BR>_______________________________________________<BR>Bioinformatics.Org
general forum - <A
onclick="return top.js.OpenExtLink(window,event,this)"
href="mailto:BiO_Bulletin_Board@bioinformatics.org" target=_blank>
BiO_Bulletin_Board@bioinformatics.org</A><BR><A
onclick="return top.js.OpenExtLink(window,event,this)"
href="https://bioinformatics.org/mailman/listinfo/bio_bulletin_board"
target=_blank>https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
</A><BR></BLOCKQUOTE></DIV><BR><BR clear=all><BR>-- <BR>-- <BR>Martin
Gollery<BR>Associate Director<BR>Center For Bioinformatics<BR>University of
Nevada at Reno<BR>Dept. of Biochemistry / MS330<BR>775-784-7042<BR>-----------
</BLOCKQUOTE></BODY></HTML>