Does Fasta Produce A Local Or Global Alignment?
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10.2 years ago
Christian ★ 3.0k

People get confused about this seemingly simple question. I hear people saying that BLAST performs a local alignment, but FASTA performs a global alignment. Also, historically there seem to be different versions of FASTA with different behaviour. I would like to hear an expert opinion on this.

fasta pairwise local alignment • 4.6k views
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10.2 years ago
Neilfws 49k

You don't have to be an expert; it's right there on the web pages and in the documentation.

FASTA

The FASTA programs find regions of local or global (new) similarity between Protein or DNA sequences

So originally, FASTA did perform local alignment, but more recent versions also perform global. You can also read the changelog to see revisions over time.

BLAST

The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences

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I think we have to differentiate here between different programs of the FASTA package. It seems the statement above from the University of Virginia regarding the capability of FASTA to perform global alignments refers to the more recent 'ggsearch' program of the FASTA package.

But what about the FASTA program of the FASTA package? Is it correct to say that it performs local alignment only? And has it always been so?

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I guess there is FASTA "the suite" and FASTA "the program in the suite". So the former provides (recently) global search, the latter local.

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