Description

Repeat Masker track constructed with the HMMER alignment engine and Dfam_3.1 database.

RepeatMasker version 4.1.0
Search Engine: HMMER [ 3.2.1 (June 2018) ]
RepeatMasker Database: HMM-Dfam_3.1

Display Conventions and Configuration

Color is based on repeat name or family:

Repeat	Color	Repeat	Color
(CATTC)n		(GAATC)n
ALR/Alpha		BSR/Beta
CER		DNA
GSAT		HSAT
LINE		Low_complexity
LSAU		LTR
RC/Helitron		Retroposon
RNA		rRNA
SAR		Satellite/acro
Satellite/telo		SATR1
scRNA		Simple repeat
SINE		snRNA
srpRNA		SSTI
SUBTEL_sa		tRNA
Unknown

Methods

RepeatMasker with Dfam.

Credits

Thanks to Arian Smit, Robert Hubley, and the Dfam project for providing the tools and models used to generate this track.

References

Smit AFA, Hubley R, Green P. RepeatMasker Open-3.0. http://www.repeatmasker.org. 1996-2010.

Smit AF. The origin of interspersed repeats in the human genome. Curr Opin Genet Dev. 1996 Dec;6(6):743-8. PMID: 8994846

Robert Hubley; Robert D. Finn; Jody Clements; Sean R. Eddy; Thomas A. Jones; Weidong Bao; Arian F.A. Smit; Travis J. Wheeler The Dfam database of repetitive DNA families Nucleic Acids Research (2016) Database Issue 44:D81-89. DOI: 10.1093/nar/gkv1272

For a discussion of repeats in mammalian genomes, see:

Smit AF. Interspersed repeats and other mementos of transposable elements in mammalian genomes. Curr Opin Genet Dev. 1999 Dec;9(6):657-63. PMID: 10607616