Minimal perfect hash functions in large scale bioinformatics Problem

Antoine Limasset (1) , Camille Marchet (1) , Pierre Peterlongo (1) , Lucie Bittner (2, 3, 4)

1 GenScale - Scalable, Optimized and Parallel Algorithms for Genomics
2 AD2M - Adaptation et diversité en milieu marin
3 IBENS - Institut de biologie de l'ENS Paris
4 IBPS - Institut de Biologie Paris Seine

. Genomic and metagenomic fields, generating huge sets of short genomic sequences, brought their own share of high performance problems. To extract relevant pieces of information from the huge data sets generated by current sequencing techniques, one must rely on extremely scalable methods and solutions. Indexing billions of objects is a task considered too expensive while being a fundamental need in this field. In this paper we propose a straightforward indexing structure that scales to billions of element and we propose two direct applications in genomics and metagenomics. We show that our proposal solves problem instances for which no other known solution scales-up. We believe that many tools and applications could benefit from either the fundamental data structure we provide or from the applications developed from this structure.

Domaines: Bio-informatique [q-bio.QM]; Algorithme et structure de données [cs.DS]

Antoine Limasset, Camille Marchet, Pierre Peterlongo, Lucie Bittner. Minimal perfect hash functions in large scale bioinformatics Problem. JOBIM 2016, Jun 2016, Lyon, France. ⟨hal-01341718⟩