See also weak hits, -maxhits option.

Termination conditions are combined with OR, so the first one to be satisfied causes the search to stop. (Unlike accept criteria, which are combined with AND).

By default, termination options are enabled only for clustering and search commands based on the USEARCH algorithm. This is because USEARCH tests database sequences (targets) in order of decreasing number of words in common between the query and target sequence. This order correlates well with sequence similarity, so the best hit(s) are likely to be found quickly.

With ublast, search_local and search_global, targets are compared to the query in an order that does not correlate with sequence similarity or E-value. With these commands, the first accepted hit is not expected to be close to the best possible hit. However, termination options can still be useful; see weak hits for discussion and examples.

If maxaccepts is set to a value > 1, then more than one hit may be reported per query. In this case, it is usually recommended to increase maxrejects also, because it will often be necessary to search further into the list of candidate target sequences to find more than one hit.

The maxaccepts and maxrejects options can be used to tune speed against sensitivity. Smaller values of both parameters tend to improve speed by reducing the number of alignments that must be computed per query. For example, with cluster_fast, the default value of maxrejects is reduced from 32 to 8 in order to achieve higher speed. Increasing either value tends to result in slower execution because more alignments must be computed. Increasing maxrejects tends to improve sensitivity by reducing the number of false negatives, i.e. target sequences that would be accepted but are not tested because they are too far down the list in word-count order.

With translated searches, termination conditions apply to each ORF separately. This is because the nucleotide query sequence might span more than one gene.