[BiO BB] Re: PSI-BLAST query filter
idoerg at burnham.org
Thu Mar 10 12:37:24 EST 2005
The first round of PSI-BLAST is actually a regular BLASTP, but which
generates a position specific score matrix. (NOT a consensus sequence).
The second round is an alignment to the PSSM, generateing a new PSSM,
and so on, ad nauseum or convergence (i.e. no new sequences).
You are right, neither is a true multiple alignment.
Kevin Berney wrote:
>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.
>OK, I still do not understand why blastpgp insists on
>sequence... which version are you using?
>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
>3) If those two factors do not matter, then why not
>use blastall to build
>your alignment? Why do oyu need the iterations
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Iddo Friedberg, Ph.D.
The Burnham Institute
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The First Automated Protein Function Prediction SIG
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