I don't know if any of you came across that problem before but when I do a blast of one genome against a database (with the 2nd genome) I get a blast against only one of the contigs in the output. I am not sure whether the blast didn't work or if I just have to change the ACT display. I tried megablast and blastn as tasks with the same result. I know this result can't be because the genomes I am comparing is the draft vs the final assembly so there should be blast hits all the way.
Thank you very much in advance, Cheers