I'm using b2g4pipe for annotation of genomes. The first step is run blastx against some db (nr, swissprot, est, refseq), generating one xml file for each blastx_run, using parameter "-max_target_seqs 20". Therefore, each blastx will result in maximum 20 hits. When running b2g4pipe, I inform the directory containing the xml files generated by blastx.
My question is: how blast2go defines what the best blast hit the different database that will for mapping GO? Or better: how to set the priority of the hits in different databases? (eg: first Swissprot, second RefSeq, third NR, ...)
Could be clear in my question?
Anybody help me?