Chapter

Algorithms in Bioinformatics

Volume 6833 of the series Lecture Notes in Computer Science pp 270-281

Indexing Finite Language Representation of Population Genotypes

  • Jouni SirénAffiliated withHelsinki Institute for Information Technology (HIIT) &, Department of Computer Science, University of Helsinki
  • , Niko VälimäkiAffiliated withHelsinki Institute for Information Technology (HIIT) &, Department of Computer Science, University of Helsinki
  • , Veli MäkinenAffiliated withHelsinki Institute for Information Technology (HIIT) &, Department of Computer Science, University of Helsinki

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Abstract

We propose a way to index population genotype information together with the complete genome sequence, so that one can use the index to efficiently align a given sequence to the genome with all plausible genotype recombinations taken into account. This is achieved through converting a multiple alignment of individual genomes into a finite automaton recognizing all strings that can be read from the alignment by switching the sequence at any time. The finite automaton is indexed with an extension of Burrows-Wheeler transform to allow pattern search inside the plausible recombinant sequences. The size of the index stays limited, because of the high similarity of individual genomes. The index finds applications in variation calling and in primer design.