Blixem_X in the ?Method

Richard Durbin rd at sanger.ac.uk
Fri May 28 17:13:14 EST 1999


You can store the target sequences inside acedb as DNA or peptide
objects.  Then blixem gets them internally and does not use
efetch. This is substantially faster as well, but can make your acedb
database large.

Alternatively, there is a fairly simple program efetchindex to make
efetch indices for any fasta database.  Contact Erik.Sonnhammer at cgr.ki.se
for details.

Finally, you can use any indexing system of your own that you want,
and write an efetch emulator that you put in your path.  I think all
it needs is to take the identifier as the argument with an option -q
that you can ignore, and return the sequence without any additional
characters (no linebreaks or anything).

Richard



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