fasta,last

[huda]

hi,

 

I'm confused with FASTA, BLAST

Are it software or format.

 

what is it's relationship with global and local alignment.

 

 

 

can anyone help. thanks

[CharonY]

Fasta is a file format, blast is an algorithm, essentially a local alignment tool, but it is more useful for searching large data sets as, say, Smith-Waterman. For details read up on Altschul et al (1990 J Mol Biol 215 (3)).

[huda]

Fasta is a file format, blast is an algorithm, essentially a local alignment tool, but it is more useful for searching large data sets as, say, Smith-Waterman. For details read up on Altschul et al (1990 J Mol Biol 215 (3)).

 

But, I think that FASTA a file format and also software .

 

I read much about file formats and I found there are many formats.

how can we choice the file formats?

how can know that is best for our sequence?

 

tanks in advance

[CharonY]

Ah the FASTA algorithm (which is also the origin of the fasta file format, forgot about that). Right, that one is actually based on Smith-Waterman (IIRC). The required file formats are dependent on the software. The majority of alignment tools use fasta (the file format).

 

This is clearly not a biological issue, and I move it to the computational section.