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 |
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Keywords
- Chromosome-wide
- Mammalian genome
- Mining
- RE array
- REMiner-II
- Repetitive element
ASJC Scopus subject areas
- Genetics
Cite this
REMiner-II : A tool for rapid identification and configuration of repetitive element arrays from large mammalian chromosomes as a single query. / Kim, Woo Chan; Lee, Kang Hoon; Shin, Kyung Seop; You, Ri Na; Lee, Young Kwan; Cho, Kiho; Cho, Dong Ho.
In: Genomics, Vol. 100, No. 3, 09.2012, p. 131-140.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - REMiner-II
T2 - A tool for rapid identification and configuration of repetitive element arrays from large mammalian chromosomes as a single query
AU - Kim, Woo Chan
AU - Lee, Kang Hoon
AU - Shin, Kyung Seop
AU - You, Ri Na
AU - Lee, Young Kwan
AU - Cho, Kiho
AU - Cho, Dong Ho
PY - 2012/9
Y1 - 2012/9
N2 - 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.
AB - 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.
KW - Chromosome-wide
KW - Mammalian genome
KW - Mining
KW - RE array
KW - REMiner-II
KW - Repetitive element
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U2 - 10.1016/j.ygeno.2012.06.006
DO - 10.1016/j.ygeno.2012.06.006
M3 - Article
C2 - 22750555
AN - SCOPUS:84865348559
VL - 100
SP - 131
EP - 140
JO - Genomics
JF - Genomics
SN - 0888-7543
IS - 3
ER -