The Wellcome Trust Centre for Human Genetics University of Oxford

Statistics of Sequence and Profile Alignments

This page contains information on methods for assessing statistical significance of protein-protein and protein-profile similarities, based around the theoretical ideas in Mott and Tribe 1999, "Approximate Statistics of Gapped Alignments" J. Comp. Biol 6:91-112, and Mott, 2000, Accurate Formula for P-values of gapped local sequence and profile alignments J. Mol Biol. 300:649-659 [link to JMB]

This work has now been extended to give a robust and accurate formula for assessing statistical significance, described here.

A software implementation called ARIADNE is available for download. Full documentation and data are available.

Related work, on alignments with non-affine gap penalties is described here.

Contact Richard Mott for more details.