What Makes Fft Appropriate For Multiple Sequence Alignment But Not Mapping?

Question

[Jeremy Leipzig]

A loaded question, to be sure, but the Fast Fourier Transform is a big part of MAFFT but doesn't get much usage elsewhere. Why isn't FFT appropriate as a general search heuristic?

Is there a FFT-BLAST I don't know about?

Answer 1

[Istvan Albert]

Your question intrigued me a bit so a read a good part of MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform here is something that may be the answer:

By the FFT analysis, however, we can know only the positional lag k of a homologous region in two sequences but not the position of the region.