About MicrobesOnline Sequence Search
To search for a sequence in MicrobesOnline, click here.
MicrobesOnline sequence search first looks for near-exact matches by using BLAT, which is very fast. This can find sequences that match protein queries even if no gene was annotated.
Next, sequence search uses FastHMM to find domains & families. (It searches for hits to COG, Pfam, TIGRFam, Superfamily, Gene3D, and PIRSF, but not Panther.)
Finally, sequence search uses "FastBLAST" to find distant protein homologs. FastBLAST relies on the domains and families to find potential homologs. For regions that do not belong to any families, it uses BLAST against sequences that do not belong to families to find potential homologs. Given these potential homologs, FastBLAST uses BLASTp to rank the hits.
You can also BLAST against MicrobesOnline databases, but BLAST is much slower than sequence search.
The nucleotide search uses MEGABLAST against all of the genomes in the MicrobesOnline database. You can BLAST
against MicrobesOnline databases instead if this is not sensitive enough.