Hi
> As far as I saw, FASTA does not have a sequence-against-sequence mode,
> only sequence-against-database?
No, thats not true. You can compare a sequence against a sequence or against a
database with fasta.
Maybe you should try the online version of fasta for comparing two sequences:
http://fasta.bioch.virginia.edu/fasta_www/cgi/search_frm2.cgi
Hope this helps,
Andrea
--
http://www.bioinformatik.de
