AluMine: alignment-free method for the discovery of polymorphic Alu element insertions.

ABSTRACT:

Background

Recently, alignment-free sequence analysis methods have gained popularity in the field of personal genomics. These methods are based on counting frequencies of short k-mer sequences, thus allowing faster and more robust analysis compared to traditional alignment-based methods.

Results

We have created a fast alignment-free method, AluMine, to analyze polymorphic insertions of Alu elements in the human genome. We tested the method on 2,241 individuals from the Estonian Genome Project and identified 28,962 potential polymorphic Alu element insertions. Each tested individual had on average 1,574 Alu element insertions that were different from those in the reference genome. In addition, we propose an alignment-free genotyping method that uses the frequency of in

SUBMITTER: Puurand T 

PROVIDER: S-EPMC6639938 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature