Data structures and compression algorithms for genomic sequence data.

ABSTRACT:

Motivation

The continuing exponential accumulation of full genome data, including full diploid human genomes, creates new challenges not only for understanding genomic structure, function and evolution, but also for the storage, navigation and privacy of genomic data. Here, we develop data structures and algorithms for the efficient storage of genomic and other sequence data that may also facilitate querying and protecting the data.

Results

The general idea is to encode only the differences between a genome sequence and a reference sequence, using absolute or relative coordinates for the location of the differences. These locations and the corresponding differential variants can be encoded into binary strings using various entropy coding methods, from fixed codes such as Gol

SUBMITTER: Brandon MC 

PROVIDER: S-EPMC2705231 | biostudies-literature | 2009 Jul

REPOSITORIES: biostudies-literature