Partially local three-way alignments and the sequence signatures of mitochondrial genome rearrangements.

ABSTRACT:

Background

Genomic DNA frequently undergoes rearrangement of the gene order that can be localized by comparing the two DNA sequences. In mitochondrial genomes different mechanisms are likely at work, at least some of which involve the duplication of sequence around the location of the apparent breakpoints. We hypothesize that these different mechanisms of genome rearrangement leave distinctive sequence footprints. In order to study such effects it is important to locate the breakpoint positions with precision.

Results

We define a partially local sequence alignment problem that assumes that following a rearrangement of a sequence F, two fragments L, and R are produced that may exactly fit together to match F, leave a gap of deleted DNA between L

SUBMITTER: Al Arab M 

PROVIDER: S-EPMC5569537 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature