For some query sequences, the top orthology values are low.

This is useful for query sequences that are appear to have no orthologs in the current databases.

The method is slower but more sensitive at lower values of k, which are also preferred for searches involving a very short query sequence.

When used as a query sequence, it returns no significant hits.

These known complex structures are then used as templates to structurally model the interaction between query sequences.

Make a k-letter word list of the query sequence.

Repeat step 3 to 4 for each k-letter word in the query sequence.

Thus, sometimes several homology models are produced for a single query sequence, with the most likely candidate chosen only in the final step.

A 200-residue query sequence with ktup2 uses a value 28.

It uses the index to find regions in the genome likely to be similar to the query sequence.