bfindex, bfind - build Bloom filter for a set of sequences, and search. bfindex: for all files/sequences in input, build a bloom filter, write to file bfind: load bf from file; for all sequences in input, match against filter and generate output. Indexed k sequences of total lenght m, query with l sequences size n. Indexing: O(m) time, O(m/k) avg/expected space. Output hit counts: O(k*n) time, O(k) space. (E.g. expr analysis) Output hit sequences (ref based clustering): O(k*n) time, O(l) space.