[Guiblast-devel] Assistance

[Sebastian Bassi]

hua pan wrote:

> I am still quite not sure what need to do. Definitely, there are a lot 
> need to be done. Should we implement all the blast program located in 
> http://www.ncbi.nlm.nih.gov/BLAST/producttable.html ? In realizing the 

Yes, that would be the ideal. There's already a scroll down menu with 
the options of the diferent program names (blastp is selected by 
default). The problem I see is that the database should be somehow 
syncronised with the program, since some programs are required diferrent 
databses. Eg. If program es blastn, databse should be nucleotide type.

> code, will we call BlastallCommandline from Application.py, blastall 
> from NCBIStandalone.py or we just directly execute the blast program 
> with options?

I'd like to see pro and cons of diferent options. The program now calls 
the function on NCBIStandalone.py and then this function calls the blastall.

> Sebastian, in your convinience, could you send us a more detailed Doc. 
> as our first design doc? Such as the whole graph overview of GUI blast.

Ok, I'll do it as fast as I can (I want to do it fast, but this is not 
always possible.

> BTW, I am planning to take part in the tutorial session of 
> http://conferences.computer.org/bioinformatics/CSB2003/TutorAbs.html#AM3. 
> I think it will help me to understand blast better. If we have 
> questions, we can ask the speacker directly. What do you think?

It would be very good. Here is the question I would ask: Could you 
please tell me blast parameters to make different strict or lax search?
For example: Making "word" parameter bigger, the search is more 
specific. I would like to know more about this. Anyway, this could be 
resolved with several tries (try and error).


-- 
Best regards,

//=\ Sebastian Bassi - Diplomado en Ciencia y Tecnologia, UNQ   //=\
\=// IT Manager Advanta Seeds - Balcarce Research Center -      \=//
//=\ Pro secretario ASALUP - www.asalup.org - PGP key available //=\
\=// E-mail: sbassi@genesdigitales.com - ICQ UIN: 3356556 -     \=//

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