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Multi-allelic positional Burrows-Wheeler transform.
- Source :
-
BMC Bioinformatics . 6/6/2019 Supplement 11, Vol. 20 Issue 11, p1-8. 8p. 1 Diagram, 10 Charts. - Publication Year :
- 2019
-
Abstract
- Background: 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. 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. Results: In 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. Conclusion: Considering 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. [ABSTRACT FROM AUTHOR]
Details
- Language :
- English
- ISSN :
- 14712105
- Volume :
- 20
- Issue :
- 11
- Database :
- Academic Search Index
- Journal :
- BMC Bioinformatics
- Publication Type :
- Academic Journal
- Accession number :
- 136827410
- Full Text :
- https://doi.org/10.1186/s12859-019-2821-6