Perhaps the most well known application of sequence matching is the testing of DNA or protein sequences against genome databases.
Gene names were assigned on the basis of the best sequence match to a human gene identified by BLAST.
However, since matching AGIs are predicted on the basis of sequence homology, it is possible that similar sequences may encode proteins with different functions and conversely, that divergent sequences encode proteins with similar functions.
On the basis of sequence analysis, these proteins are IMPs with 12 TMHs (excluding the possible signal peptide), and match with four, seven and three unique peptides, respectively.
The structural basis underlying these distinctive transport mechanisms is puzzling because CLC channels and transporters are expected to share the same architecture on the basis of sequence homology.
If the Nipponbare genome had been used, flanking primer sequences were used as queries in a BLASTN search, and the locations of both primers were determined on the basis of perfect match alignment between the primers and Nipponbare genome sequences.
Using GO/UniProt comparison tables (gene_association.goa_uniprot, Apr 2010), candidate GO assignments were predicted on the basis of contig matches to the UniProt reference sequences.
On the basis of this sequence information, we coded in-house Perl scripts to match possible E-box and BRRE motif in upstream 3,000 bp region by searching conserved sequence 'CANNTG' for general E-box or CATGTG for specific E-box and conserved sequence 'CGTG(T/C G' for the BRRE site.
At >62.50% similarity, 3 main clusters were found that matched with existing species on the basis of multilocus sequence analysis (ITS, CDC42, BT2, and ACT1), i.e., F. pedrosoi, F. monophora, and F. nubica.
