The HOMD BLAST server uses SequenceServer to provide local BLAST resources that employ various HOMD databases. You can BLAST against the HOMD 16S rRNA RefSeq sequences or choose to BLAST against HOMD genomes. For HOMD genomes you have the option of BLASTing against a database of all HOMD genomes combined or choosing to BLAST against a single HOMD genome of your choice.

Available BLAST Help Pages:

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Blast Formats
Blast Databases
Blast Parameters
Blast Programs
Blast Advanced
NCBI BLAST® Command Line Applications User Manual (linkout)