Problem loading database in ACT

[cascoamarillo]

Hi all,

After blast my query against my database (compose by contigs), I've tried to see the homologies in the Artemis Comparison Tool (ACT) by loading the query, the blastout (doing blast with -m 8 flag) and my original database; but the problem is that this database is quite large (200Mb) and it doesn't load into ACT.
So I'm thinking how to filter the database and take only the contigs that have some homologies. Any ideas?? Maybe a script or any program?

Thanks!

[Torst]

After blast my query against my database (compose by contigs), I've tried to see the homologies in the Artemis Comparison Tool (ACT) by loading the query, the blastout (doing blast with -m 8 flag) and my original database; but the problem is that this database is quite large (200Mb) and it doesn't load into ACT.

Did ACT tell you it was out of memory? If so, follow the instructions for allocating more RAM to the JVM running ACT - just look at FAQ at the ACT site: http://www.sanger.ac.uk/resources/software/artemis/

Also, you may want to reduce the size of the blast output by making your "-e" evalue smaller, or using "-v/-b" to limit the number of HSPs in repetitive regions.

[cascoamarillo]

thanks for the ideas!
But it doesn't tell me it's out of memory; it starts loading the seqs but it never ends.
To reduce the size of the output is a good point, I've tried it ; unfortunately the database is still huge. Now I'm selecting contigs, almost manually, just to make some comparisons.