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Thanks to Eileen Hamilton's urging, NCBI has improved the blast resources for the T. thermophila
macro- and micronuclear genomes.  The scaffolds from each genome assembly are now present and
in separate databases, so they can be searched separately.  See the new blast website at:
http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?
PAGE_TYPE=BlastSearch&PROG_DEF=blastn&BLAST_PROG_DEF=megaBlast&BLAST_SPEC=OGP__5911_
_12563