Blast format change at NCBI

[Peter Rice]

NCBI's FTP server will be releasing BLAST formatted databases in a new
format (version 4) from February 19th.

This format is not supported by EMBOSS dbiblast indexing (or by NCBI's
blastall before the current version 2.2.2)

See ftp://ftp.ncbi.nih.gov/blast/db/NewFormattedDatabases/README

If you have the fasta format files, you should be able to use dbifasta to
index the same entries.

The blast 2.2.2 release notes say "Fastacmd will dump out an entire BLAST
database in FASTA format if the new -D option is used", but I have not
tried this yet to see how well it fits with EMBOSS.

Has anyone else looked into this yet?

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Peter Rice, LION Bioscience Ltd, Cambridge, UK
peter.rice at uk.lionbioscience.com +44 1223 224723