AlleleHMM: a data-driven method to identify allele specific differences in distributed functional genomic marks.

ABSTRACT: How DNA sequence variation influences gene expression remains poorly understood. Diploid organisms have two homologous copies of their DNA sequence in the same nucleus, providing a rich source of information about how genetic variation affects a wealth of biochemical processes. However, few computational methods have been developed to discover allele specific differences in functional genomic data. Existing methods either treat each SNP independently, limiting statistical power, or combine SNPs across gene annotations, preventing the discovery of allele specific differences in unexpected genomic regions. Here we introduce AlleleHMM, a new computational method to identify blocks of neighboring SNPs that share similar allele specific differences in mark abundance. AlleleHMM uses a hidden Mar

SUBMITTER: Chou SP 

PROVIDER: S-EPMC6582321 | biostudies-literature | 2019 Jun

REPOSITORIES: biostudies-literature