Complete Parsimony Haplotype Inference Problem and Algorithms
2009 (English)In: Proceedings of 17th Annual European Symposium on Algorithms (ESA 2009) / [ed] A. Fiat and P. Sanders, Berlin-Heidelberg: Springer Berlin-Heidelberg , 2009, 337-348 p.Conference paper (Refereed)
Haplotype inference by pure parsimony (HIPP) is a wellknown paradigm for haplotype inference. In order to assess the biological significance of this paradigm, we generalize the problem of HIPP to the problem of finding all optimal solutions, which we call complete HIPP. We study intrinsic haplotype features, such as backbone haplotypes and fat genotypes as well as equal columns and decomposability. We explicitly exploit these features in three computational approaches which are based on integer linear programming, depth-first branch-and-bound, and a hybrid algorithm that draws on the diverse strengths of the first two approaches. Our experimental analysis shows that our optimized algorithms are significantly superior to the baseline algorithms, often with orders of magnitude faster running time. Finally, our experiments provide some useful insights to the intrinsic features of this interesting problem.
Place, publisher, year, edition, pages
Berlin-Heidelberg: Springer Berlin-Heidelberg , 2009. 337-348 p.
, Lecture Notes in Computer Science, Volume 5757
Bioinformatics (Computational Biology)
IdentifiersURN: urn:nbn:se:umu:diva-84448OAI: oai:DiVA.org:umu-84448DiVA: diva2:684110
17th Annual European Symposium on Algorithms (ESA 2009)