Analysis of transposable element sequences using CENSOR and RepeatMasker.

Ahsan Huda
Ahsan Huda
School of Biology

Methods Mol Biol 2009 ;537:323-36

School of Biology, Georgia Institute of Technology, Atlanta, GA, USA.

Eukaryotic genomes are full of repetitive DNA, transposable elements (TEs) in particular, and accordingly there are a number of computational methods that can be used to identify TEs from genomic sequences. We present here a survey of two of the most readily available and widely used bioinformatics applications for the detection, characterization, and analysis of TE sequences in eukaryotic genomes: CENSOR and RepeatMasker. For each program, information on availability, input, output, and the algorithmic methods used is provided. Specific examples of the use of CENSOR and RepeatMasker are also described. CENSOR and RepeatMasker both rely on homology-based methods for the detection of TE sequences. There are several other classes of methods available for the analysis of repetitive DNA sequences including de novo methods that compare genomic sequences against themselves, class-specific methods that use structural characteristics of specific classes of elements to aid in their identification, and pipeline methods that combine aspects of some or all of the aforementioned methods. We briefly consider the strengths and weaknesses of these different classes of methods with an emphasis on their complementary utility for the analysis of repetitive DNA in eukaryotes.

Download full-text PDF

Source Listing

Still can't find the full text of the article?

Sign up to send a request to the authors directly.
August 2009
6 Reads

Publication Analysis

Top Keywords

censor repeatmasker
repetitive dna
classes methods
eukaryotic genomes
genomic sequences
analysis repetitive
novo methods
methods compare
sequences classes
including novo
detection sequences
sequences including
methods analysis
dna sequences
rely homology-based
methods provided
algorithmic methods

Similar Publications

The Epidemiology of Unintentional and Violence-Related Injury Morbidity and Mortality among Children and Adolescents in the United States.

Int J Environ Res Public Health 2018 03 28;15(4). Epub 2018 Mar 28.

The Bizzell Group, LLC, Lanham, MD 20706, USA.

Injuries and violence among young people have a substantial emotional, physical, and economic toll on society. Understanding the epidemiology of this public health problem can guide prevention efforts, help identify and reduce risk factors, and promote protective factors. We examined fatal and nonfatal unintentional injuries, injuries intentionally inflicted by other (i. Read More

View Article
March 2018
4 Reads
1 PubMed Central Citation(source)
2.06 Impact Factor

N,N-Disubstituted-N'-acylthioureas as modular ligands for deposition of transition metal sulfides.

Dalton Trans 2018 Feb;47(8):2719-2726

Department of Chemistry, University of Florida, Gainesville, Florida 32611, USA.

First row transition metal complexes (Ni, Co, Cu, Zn) with N,N-disubstituted-N'-acylthiourea ligands have been synthesized and characterized. Bis(N,N-diisopropyl-N'-cinnamoylthiourea)nickel was found to have the lowest onset temperature for thermal decomposition. Thin film deposition of Ni, Co, and Zn sulfides by aerosol assisted chemical vapor deposition from their respective N,N-diisopropyl-N'-cinnamoylthiourea complexes at 350 °C has been demonstrated. Read More

View Article
February 2018
60 Reads
4.20 Impact Factor

Blood-based biomarkers of adverse perinatal outcomes in maternal obesity.

J Matern Fetal Neonatal Med 2017 Dec 12;30(24):2991-2997. Epub 2017 Jan 12.

c Centro de Neurociencias y Unidad de Investigación Clínica , Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP) , Clayton , Panamá.

Objective: Increasing maternal weight has been shown to predict adverse perinatal outcome, including increases in the relative risk of fetal death, stillbirth, neonatal death, perinatal death and infant death. In order to better understand the pathophysiological factors associated with obesity during pregnancy, the role of biomarkers associated with adverse outcomes in obese pregnant women is under investigation. The purpose of this review study was to examine potential biomarkers that could serve as effective screening strategies in obese pregnant women to reduce fetal and neonatal morbidity, as well as maternal morbidity. Read More

View Article
December 2017
4 Reads

A PARP1-ERK2 synergism is required for the induction of LTP.

Sci Rep 2016 04 28;6:24950. Epub 2016 Apr 28.

Neufeld Cardiac Research institute, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv 69978, Israel.

Unexpectedly, a post-translational modification of DNA-binding proteins, initiating the cell response to single-strand DNA damage, was also required for long-term memory acquisition in a variety of learning paradigms. Our findings disclose a molecular mechanism based on PARP1-Erk synergism, which may underlie this phenomenon. A stimulation induced PARP1 binding to phosphorylated Erk2 in the chromatin of cerebral neurons caused Erk-induced PARP1 activation, rendering transcription factors and promoters of immediate early genes (IEG) accessible to PARP1-bound phosphorylated Erk2. Read More

View Article
April 2016
5 Reads
3 PubMed Central Citations(source)
5.08 Impact Factor

[Medical treatment of ectopic pregnancy].

Tunis Med 2013 Jul;91(7):435-9

Background: The ectopic pregnancy (EP) is a public health problem and its frequency has doubled in most industrialized countries in 20 years. aim: To evaluate the effectiveness of medical treatment of ectopic pregnancy with methotrexate (MTX) intramuscularly (IM).

Methods: prospective study supported between October 2006 and December 2010. Read More

View Article
July 2013
3 Reads