Pattern matching for high precision detection of LINE-1s in human genomes.

ABSTRACT:

Background

Long interspersed element 1 (LINE-1 or L1) retrotransposons are mobile elements that constitute 17-20% of the human genome. Strong correlations between abnormal L1 expression and several human diseases have been reported. This has motivated increasing interest in accurate quantification of the number of L1 copies present in any given biologic specimen. A main obstacle toward this aim is that L1s are relatively long DNA segments with regions of high variability, or largely present in the human genome as truncated fragments. These particularities render traditional alignment strategies, such as seed-and-extend inefficient, as the number of segments that are similar to L1s explodes exponentially. This study uses the pattern matching methodology for more accurate identificat

SUBMITTER: Lopez JO 

PROVIDER: S-EPMC9472350 | biostudies-literature | 2022 Sep

REPOSITORIES: biostudies-literature