Abstract
Genes occupy ~. 3% of the human and mouse genomes whereas repetitive elements (REs), whose biologic functions are largely uncharacterized, constitute greater than 50%. A heterogeneous population of RE arrays (arrangement structures) is formed by combinations of various REs in mammalian genomes. In this study, REMiner-II was refined from the original REMiner for a more efficient identification and configuration of RE arrays from large queries (e.g., human chromosomes) using an unbiased self-alignment protocol. Chromosome-wide RE array profiles for the entire sets of human and mouse chromosomes were obtained using REMiner-II on a personal computer. REMiner-II provides 10 adjustable parameters and three data output modes to accommodate different experimental settings and/or goals. Examination of the human and mouse chromosome data using the REMiner-II viewer revealed species-specific libraries of complexly organized RE arrays. In conclusion, REMiner-II is an efficient tool for chromosome-wide identification and characterization of RE arrays from mammalian genomes.
Original language | English (US) |
---|---|
Pages (from-to) | 131-140 |
Number of pages | 10 |
Journal | Genomics |
Volume | 100 |
Issue number | 3 |
DOIs | |
State | Published - Sep 2012 |
Keywords
- Chromosome-wide
- Mammalian genome
- Mining
- RE array
- REMiner-II
- Repetitive element
ASJC Scopus subject areas
- Genetics