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Performance comparisons of blast and fasta programs?

Fredj Tekaia tekaia at pasteur.fr
Tue Apr 13 07:00:10 EST 1993

Dear Netter,

I am interrested in comparing the performances of the 2 family programs :
BLAST and FASTA. Performances in terms of speed of execution and accuracy
of the results.
The question has been posted some time ago by David Kristofferson but had
received little comments may be because at that time there are many fasta
users and few users of the new blast programs.  Now with the ncbi server may be
there are more people who experienced the blast programs.

I know some advantages in favour of the blast programs :
a) time of execution (fast), b) statistical evaluation of the results
c) report several matches per sequence (fasta reports only the best match)
But this is not enough for comparing!

Can experienced people with these 2 family programs comment the
advantages and drawbacks of each of them if any?
(eventually point to papers dealing with the question)

In fact I would like to know if for comparing a test sequence to a database :
Is it best to do it by :
a) fasta programs, b) the blast programs or c) both programs?

Thanks for any comment.

Fredj Tekaia

Fredj Tekaia				Service d`Informatique Scientifique
tekaia at pasteur.fr			Institut Pasteur
					25, rue du Dr. Roux
					75724 Paris cedex 15	France

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