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<TITLE>FW: Evolutionary pathway from seq alignment</TITLE>
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<P><FONT FACE="Times New Roman"></FONT> <FONT SIZE=1 FACE="Tahoma">-----Original Message-----</FONT>
<BR><B><FONT SIZE=1 FACE="Tahoma">From: </FONT></B> <FONT SIZE=1 FACE="Tahoma">Goel, Manisha </FONT>
<BR><B><FONT SIZE=1 FACE="Tahoma">Sent: </FONT></B> <FONT SIZE=1 FACE="Tahoma">Tuesday, August 24, 2004 2:29 PM</FONT>
<BR><B><FONT SIZE=1 FACE="Tahoma">To: </FONT></B> <FONT SIZE=1 FACE="Tahoma">'pdb-l@sdsc.edu'</FONT>
<BR><B><FONT SIZE=1 FACE="Tahoma">Subject: </FONT></B> <FONT SIZE=1 FACE="Tahoma">Evolutionary pathway from seq alignment</FONT>
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<P><FONT FACE="Times New Roman">Dear All,</FONT>
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<P><FONT FACE="Times New Roman">I am quite new to sequence alignments and have a basic question (nevertheless I can’t figure it out for myself), so please help.</FONT></P>
<P><FONT FACE="Times New Roman">I am using a variety of seq alignment programs to align the output of PSI-Blast. </FONT>
<BR><FONT FACE="Times New Roman">In a particular program my query is among the top sequences and the rest of the hits with decreasing similarity arranged below.</FONT></P>
<P><FONT FACE="Times New Roman">In the other program, a few seq not so very similar to the query are at top, and then a stack of seq similar to query (including query) are arranged in the middle followed by other seqs arranged in order of lowering similarity.</FONT></P>
<P><FONT FACE="Times New Roman">Does this mean that the two programs are showing two different evolutionary pathways for the sequences picked up by PSI-Blast.</FONT></P>
<P><FONT FACE="Times New Roman">Thanks for any enlightments !</FONT>
<BR><FONT FACE="Times New Roman">- Manisha</FONT>
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