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<HTML><HEAD><TITLE>RE: Instalation and D'd problem.</TITLE>
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<DIV><FONT face=Arial size=2>Hi all,</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>I am using supermatcher to align 2 sequences, and
it seems that the order of the sequences affects the results dramatically
(see example below).</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Is that normal?</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Shibl</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Note: The following examples where build by
downloading AP000926.5 and AP001970.3 from entrez and then calling</FONT></DIV>
<DIV><FONT face=Arial size=2>supermatcher with wordlen=20, all other parameters
are kept as default.</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>########################################<BR>#
Program: supermatcher<BR># Rundate: Wed Jul 31 11:54:34 2002<BR>#
Report_file:
ap000926.supermatcher<BR>########################################<BR>#=======================================<BR>#<BR>#
Aligned_sequences: 2<BR># 1: AP000926.5<BR># 2: AP001970.3<BR># Matrix:
EDNAFULL<BR># Gap_penalty: 10.0<BR># Extend_penalty: 0.5<BR>#<BR># Length:
57265<BR># Identity: 40361/57265 (70.5%)<BR># Similarity:
40361/57265 (70.5%)<BR># Gaps: 11627/57265
(20.3%)<BR># Score: 133850.5<BR>#
<BR>#<BR>#=======================================</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>########################################<BR>#
Program: supermatcher<BR># Rundate: Wed Jul 31 11:55:10 2002<BR>#
Report_file:
ap001970.supermatcher<BR>########################################<BR>#=======================================<BR>#<BR>#
Aligned_sequences: 2<BR># 1: AP001970.3<BR># 2: AP000926.5<BR># Matrix:
EDNAFULL<BR># Gap_penalty: 10.0<BR># Extend_penalty: 0.5<BR>#<BR># Length:
52182<BR># Identity: 50101/52182 (96.0%)<BR># Similarity:
50101/52182 (96.0%)<BR># Gaps:
1463/52182 ( 2.8%)<BR># Score: 242805.0<BR>#
<BR>#<BR>#=======================================<BR></FONT></DIV></BODY></HTML>