What Type Of Sequence Search Is Fasta And Blast ?
Hi all. Could someone please tell me what kind of sequence alignment is fasta and blast search ? Is is local alignment ?
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Yes fasta is also a package developped by the Pearson lab's. You can find some info here http://faculty.virginia.edu/wrpearson/fasta/fasta_guide.pdf and download ita @ http://faculty.virginia.edu/wrpearson/fasta/fasta36/ .
Both are local alignment except fasta is more robust than blast but a little bit slower. You can also do global alignment with fasta ggsearch36.
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BLAST : Basic Local Alignment Search Tool
Fasta is a sequence format. This format was what was required for input into a very early alignment algorithm developed by Bill Pearson, as I recall. While that program has been superceded, the Fasta format is now a widely accepted standard for input to many algorithms.
well isnt there a fasta sequence alignment algorithm ?
As I indicated in my post - yes, the Fasta alignment program still exists, but is not generally chosen in bioinformatics activities as the program has been superceded by others.
I wouldn't say that the fasta program is superseded of course blast is more popular than any other alignment or even any other bioinformatics algorithm. But the fasta heuristic should be more sensitive than blast while slower.