[galaxy-user] mapping

Hi, I want to map a set of sequences (derived from RNA) against a bacterial genome. Unfortunately, the genome of Synechococcus sp. PCC 7002 consists of one chromosome and six plasmids. In MAQ I can chose only one DNA entry for mapping. In local BLAST it was possible to generate databases consisting of several DNA entries to map the data. Does anybody have experience in mapping transcription data against complex genomes in Galaxy. Best regards, Marcus