Thanks for all,
Now I undertand, :-)
See you in later email.
By
*****************************************************************
* Daniel Xavier de Sousa *
* Mestrando em Informática - PUC-Rio *
* E-MAIL : dsousaARROBAinf.puc-rio.br *
* Fone : +55 21 35271500 - 4543 *
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----- Mensagem original ----
De: Aaron Darling <[EMAIL PROTECTED]>
Para: Daniel Xavier de Sousa <[EMAIL PROTECTED]>
Cc: [EMAIL PROTECTED]
Enviadas: Segunda-feira, 26 de Março de 2007 22:08:21
Assunto: Re: Res: [Mpiblast-users] Res: Res: statistics of MPIBlast
mpiblast doesn't actually execute the blastall command, instead it calls
a C language function from the NCBI Toolbox code.
The functions that mpiblast calls for computing the search space would
compute the same statistics as the series of commands you list below,
but without actually performing the search.
So yes, it's similar in spirit to the commands you've listed below, but
not quite the same.
-aaron
Daniel Xavier de Sousa wrote:
> Hi Aaron Darling and Mike
>
> This is my last question (about this), I promes:
>
> When the mpiBLAST pass all fragment to get search space statistics, is
> like:
>
> blastall -p blastp -i Seq1 -d [fragment_1 fragment_2 .... fragment_n]
> blastall -p blastp -i Seq2 -d [fragment_1 fragment_2 .... fragment_n]
> blastall -p blastp -i Seq3 -d [fragment_1 fragment_2 .... fragment_n]
> ...
> blastall -p blastp -i SeqN -d [fragment_1 fragment_2 .... fragment_n]
>
> Daniel
> *****************************************************************
> * Daniel Xavier de Sousa *
> * Mestrando em Informática - PUC-Rio *
> * E-MAIL : dsousaARROBAinf.puc-rio.br *
> * Fone : +55 21 35271500 - 4543 *
> ****************************************************************
>
>
> ----- Mensagem original ----
> De: Aaron Darling <[EMAIL PROTECTED]>
> Para: [email protected]
> Enviadas: Terça-feira, 27 de Março de 2007 1:07:04
> Assunto: Re: [Mpiblast-users] Res: Res: statistics of MPIBlast
>
> Daniel Xavier de Sousa wrote:
> >
> > Hi, thank you again for your answer.
> >
> > > All of the database fragments are accessible to rank0
> >
> > If I understood, the mpiBLAST exec NCBI BLAST pass all fragments (as
> > many together) just to take statistics values, It is? And it does this
> > for each sequence of query, ok? (This last one question is the part
> > that you didn’t understand in last email)
> >
> Yes, rank 0 passes all fragments and all query sequences to the NCBI
> code in order to calculate the search space statistics.
>
> hope that helps,
> -Aaron
>
>
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