This describes how you can run blast2go on a server using b2gpipe and a local database. This makes blast2go a viable option for annotating large fasta files. Otherwise it is much too slow. The database is currently set up on an AdapTree server. This took a while for me to troubleshoot, so you could run into different problems, but you will hopefully avoid some of the issues I ran into. The b2g Google group is good for troubleshooting. You can find many of these instructions at http://www.blast2go.com/b2glaunch/resources/35-localb2gdb

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