[Biojava-l] performance problems with BJX

[Gabrielle Doan]

Dear all,
I have some perfomance problems with BioJavaX.

I wanted to add the human chromosome 1 into my MySQL database with the 
build in method addRichSequence from the 
org.biojavax.bio.db.biosql.BioSQLRichSequenceDB and was wondered why 
this method waste so much memory. I started my program with -Xmx8G but I 
got a Java heap space messseage on my console. So I used -Xmx15G to 
insert the chromsome (range between 8G and 15G not tested).

I wonder why a genbank file of about 300 MB needs about 15G memory to be 
added into the database.

Does anybody has the same problem or can give me any advice?

Cheers, Gabrielle