[ssml] FW: Evolutionary pathway from seq alignment

[Goel, Manisha]

>  -----Original Message-----
> From: 	Goel, Manisha  
> Sent:	Tuesday, August 24, 2004 2:29 PM
> To:	'pdb-l at sdsc.edu'
> Subject:	Evolutionary pathway from seq alignment
> 
> Dear All,
> 
> I am quite new to sequence alignments and have a basic question
> (nevertheless I can't figure it out for myself), so please help.
> 
> I am using a variety of seq alignment programs to align the output of
> PSI-Blast. 
> In a particular program my query is among the top sequences and the
> rest of the hits with decreasing similarity arranged below.
> 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.
> 
> Does this mean that the two programs are showing two different
> evolutionary pathways for the sequences picked up by PSI-Blast.
> 
> Thanks for any enlightments !
> - Manisha
> 
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