Psi-RA: a parallel sparse index for genomic read alignment


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Kulekci M. O. , HON W., Shah R., Vitter J. S. , Xu B.

BMC GENOMICS, cilt.12, 2011 (SCI İndekslerine Giren Dergi) identifier identifier

Özet

Background: Genomic read alignment involves mapping (exactly or approximately) short reads from a particular individual onto a pre-sequenced reference genome of the same species. Because all individuals of the same species share the majority of their genomes, short reads alignment provides an alternative and much more efficient way to sequence the genome of a particular individual than does direct sequencing. Among many strategies proposed for this alignment process, indexing the reference genome and short read searching over the index is a dominant technique. Our goal is to design a space-efficient indexing structure with fast searching capability to catch the massive short reads produced by the next generation high-throughput DNA sequencing technology.