[BiO BB] Re: PSI-BLAST query filter

[Kevin Berney]

a clarification perhaps, but doesn't psi-blast give a
list of pairwise alignments to a -- "consensus"
sequence.  or maybe a weight matrix? 

whereas blast would just give you a list of pairwise
alignments to the original query sequence.  

these ought to produce very different results.  though
neither is a true multiple alignment.

Kevin Berney



Quoting Iddo
============
OK, I still do not understand why blastpgp insists on
filtering your
sequence... which version are you using?

Not that:

1) Using blastpgp You won't get a multiple alignment.
You will get a
multiple pairwise alignment to the query sequence.
Using ClustalW you will
get a true multiple alignment.

2) There is still an inherent problem when aligning
low complexity
sequences.

3) If those two factors do not matter, then why not
use blastall to build
your alignment? Why do oyu need the iterations
blastpgp offers?

Curious,

./I

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