Formating DB's for BLAST on NT

Andrew Dalke dalke at bioreason.com
Fri Dec 11 18:32:13 EST 1998


Richard <rjacob-nospam at itsa.ucsf.edu> asked:
> For BLAST to use the database it needs to be formated with
> the "formatdb" program. Unfortunately I always obtain an error:
> [...]
> Does anyone have any clues to what I might be doing wrong or
> not doing?

If I recall, you need to have a .ncbirc (or equivalent) for
that to work.  Browsing NCBI for a bit, I think there are relevent
comments in:

  ftp://ncbi.nlm.nih.gov/blast/executables/README

Look for
> This is specified by the main configuration file for the NCBI
> toolkit (".ncbirc" on UNIX systems, ncbi.ini on Windows, analogous
> names on other platforms).

  I know, it's documentation for BLAST but I recall needing that
file for formatdb to work; probably because they are all built
from the same toolkit.

						Andrew
						dalke at bioreason.com




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