[Biojava-dev] SequenceDB way too big!!!

[Murat Tasan]

I've just started using biojava to help in my development of sequence
analysis and searching projects, but I have run into a huge (no pun
intended) problem.  I make a call to SeqIOTools.readFasta(...), to read a
FASTA file of approximately 14MB in size.  Because the file is only 14MB
or so, I figure getting a SequenceDB object from it will AT WORST take up
twice that in memory (~30MB) (with all of the extra information associated
with sequences... although my FASTA file has just sequence data).
Instead, my virtual machine eventually crashes out as I run out of memory.
I watched the execution using 'top' and witnessed over 75MB being
allocated to the running process.

Is there a more efficient implementation of this?  Better yet, can anyone
tell me why so much space is being taken up for only 14MB of sequence
data?

Thanks for any help!!!!

Murat

-- 
Murat Tasan
mxt6 at po.cwru.edu
tasan at eecs.cwru.edu
http://genomics.cwru.edu