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FASTA/TFASTA on long sequences

Guy Bottu gbottu at bigben.vub.ac.be
Wed Aug 29 12:22:44 EST 2001


I think that this is indeed the reason, that fasta makes only one
alignment. You could use blast instead, blast can report several
alignments per databank sequence. You could also, but this is of course
tedious, for each databank sequence found make an alignment with your
sequence using a program that makes suboptimal alignments (e.g. lfasta
or lalign from the fastA package version 2 or sim from Hunag and
Miller).

	Guy Bottu




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