Dinithi Sumanaweera^*, Lloyd Allison, Arun Konagurthu.

Bioinformatics, 35(14), pp.i360-i369, doi:10.1093/bioinformatics/btz368, 5 July 2019, and ISMB/ECCB 2019.

Abstract: The information criterion of minimum message length (MML) provides a powerful statistical framework for inductive reasoning from observed data. We apply MML to the problem of protein sequence comparison using finite state models with Dirichlet distributions. The resulting framework allows us to supersede the ad hoc cost functions commonly used in the field, by systematically addressing the problem of arbitrariness in alignment parameters, and the disconnect between substitution scores and gap costs. Furthermore, our framework enables the generation of marginal probability landscapes over all possible alignment hypotheses, with potential to facilitate the users to simultaneously rationalize and assess competing alignment relationships between protein sequences, beyond simply reporting a single (best) alignment. We demonstrate the performance of our program on benchmarks containing distantly related protein sequences.

Availability and implementation: The open-source program supporting this work is available from [lcb.infotech.monash.edu.au/seqmmligner].

Supplementary information: Supplementary data are available at Bioinformatics online.

^* Dinithi Sumanaweera won an 'Ian Lawson Van Toch Memorial Award for Outstanding Student Paper' at ISMB/ECCB, Basel, 2019, [www].