Finding Short Sequence Regions with Unusual Homology in Multiple, Diverse Sequences
By John McNeil
V.P. of Informatics, Ibis Therapeutics
An algorithm and software are presented which identify short (10-150 base) regions of unusually high sequence homology. This is useful for finding short sequences regions with biological function that are not otherwise identifiable. An example would be small RNA structural elements embedded in mRNAs. Starting with a version of the Compare algorithm that doesn't threshold or otherwise throw information away, the results of all possible pairwise sequence comparisons are aggregated into very local alignments. This alignment algorithm uses intermediate sequences to align regions of sequences which would normally be too divergent. An example would be finding and aligning the human IRE (Iron Response Element) to trout IRE using the chicken IRE sequence as an intermediary. The tool produces local seqeunce alignments for conserved seqeunce elements, even when element order is not conserved.