A useful feature on the ATCC Genome Portal is the k-mer based nucleotide search. The sequence search matches all k-mers (k=31) in the query against all available ATCC reference genomes and highlights portions of the sequence that match. The minimum requirement is matching 40 k-mers and 80% of the sequence to call a hit.
To use the search, simply insert a nucleotide sequence into the text box on the left and click “Search”. If any portion of your sequence matches the sequence of a published genome, it will become highlighted. To see what portion of your sequence matches the search results on the right, simply hover over a genome to highlight your sequence in the color associated with that search result.
Using the nucleotide sequence of purB from ATCC® 700610™ as an example, you can see the variation between the purB gene in two different Streptococcus mutans strains in the ATCC collection.