Abstract
BackgroundRecent advances in whole-genome sequencing and SNP array technology have led to the generation of a large amount of genotype data. Large volumes of genotype data will require faster and more efficient methods for storing and searching the data. Positional Burrows-Wheeler Transform (PBWT) provides an appropriate data structure for bi-allelic data. With the increasing sample sizes, more multi-allelic sites are expected to be observed. Hence, there is a necessity to handle multi-allelic genotype data.ResultsIn this paper, we introduce a multi-allelic version of the Positional Burrows-Wheeler Transform (mPBWT) based on the bi-allelic version for compression and searching. The time-complexity for constructing the data structure and searching within a panel containing t-allelic sites increases by a factor of t.ConclusionConsidering the small value for the possible alleles t, the time increase for the multi-allelic PBWT will be negligible and comparable to the bi-allelic version of PBWT.
Highlights
Recent advances in whole-genome sequencing and Single Nucleotide Polymorphisms (SNP) array technology have led to the generation of a large amount of genotype data
We present Positional Burrows-Wheeler Transform (PBWT) algorithms for multiallelic sites
The time for computing all long matches in our implementation was similar to the original PBWT for bi-allelic data
Summary
Recent advances in whole-genome sequencing and SNP array technology have led to the generation of a large amount of genotype data. Large volumes of genotype data will require faster and more efficient methods for storing and searching the data. There is a necessity to handle multi-allelic genotype data. The enormous amount of genotype data generated by the whole-genome sequencing or SNP arrays present a challenge to store and analyze them. Detection of large consecutive matches in a panel of genotype data is of great interest. A genotype panel is comprised of a set of alleles for multiple individuals. Genotype data in diploid organisms include the genetic information from both parents. Haplotype sequences contain the genotype information and the sequences from each parent have been separated. The naive approach for finding exact matches in a haplotype panel will require quadratic time complexity in terms of number of
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