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Parsing a huge Blast File with Biojava: msg#00000

java.bio.general

Subject:	Parsing a huge Blast File with Biojava

Hello everyone,

We are trying to parse a quite large multiple BLAST results file (around
4GB), and the computer available has 1GB of RAM. However, when the code
in the cookbook is used (
"http://www.biojava.org/docs/bj_in_anger/BlastParser.htm";), using the
BlastLikeSAXParser it will give out an OutOfMemory exception after a
short while, and when I monitor the system during the parsing, I don't
see the memory usage going up significantly. It is the
parse(InputSource) method that throws the exception. Is there a way to
solve this problem ?

Thanks,

Can

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