Cargando…

ReAS: Recovery of Ancestral Sequences for Transposable Elements from the Unassembled Reads of a Whole Genome Shotgun

We describe an algorithm, ReAS, to recover ancestral sequences for transposable elements (TEs) from the unassembled reads of a whole genome shotgun. The main assumptions are that these TEs must exist at high copy numbers across the genome and must not be so old that they are no longer recognizable i...

Descripción completa

Detalles Bibliográficos
Autores principales:	Li, Ruiqiang, Ye, Jia, Li, Songgang, Wang, Jing, Han, Yujun, Ye, Chen, Wang, Jian, Yang, Huanming, Yu, Jun, Wong, Gane Ka-Shu, Wang, Jun
Formato:	Texto
Lenguaje:	English
Publicado:	Public Library of Science 2005
Materias:	Research Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1232128/ https://www.ncbi.nlm.nih.gov/pubmed/16184192 http://dx.doi.org/10.1371/journal.pcbi.0010043

Ejemplares similares

Metabarcoding versus mapping unassembled shotgun reads for identification of prey consumed by arthropod epigeal predators
por: Paula, Débora Pires, et al.
Publicado: (2022)

The Use of RelocaTE and Unassembled Short Reads to Produce High-Resolution Snapshots of Transposable Element Generated Diversity in Rice
por: Robb, Sofia M. C., et al.
Publicado: (2013)

Expanding the spectrum of reactive arthritis (ReA): classic ReA and infection-related arthritis including poststreptococcal ReA, Poncet’s disease, and iBCG-induced ReA
por: Taniguchi, Yoshinori, et al.
Publicado: (2021)

Expression Plasticity of Transposable Elements Is Highly Associated with Organismal Re-adaptation to Ancestral Environments
por: Liu, Yan-Nan, et al.
Publicado: (2022)

A Statistical Approach Designed for Finding Mathematically Defined Repeats in Shotgun Data and Determining the Length Distribution of Clone-Inserts
por: Zhong, Lan, et al.
Publicado: (2003)

WebCARMA: a web application for the functional and taxonomic classification of unassembled metagenomic reads
por: Gerlach, Wolfgang, et al.
Publicado: (2009)

Ancestral polymorphism and recent invasion of transposable elements in Drosophila species
por: Dias, Elaine Silva, et al.
Publicado: (2012)

TAREAN: a computational tool for identification and characterization of satellite DNA from unassembled short reads
por: Novák, Petr, et al.
Publicado: (2017)

Binning unassembled short reads based on k-mer abundance covariance using sparse coding
por: Kyrgyzov, Olexiy, et al.
Publicado: (2020)

Near-optimal assembly for shotgun sequencing with noisy reads
por: Lam, Ka-Kit, et al.
Publicado: (2014)

Note from Prof. Rea
por: Rea, R. L.
Publicado: (1867)

Dr. Frank L. Rea
Publicado: (1883)

Evolutionary Transients in the Rice Transcriptome
por: Wang, Jun, et al.
Publicado: (2010)

The HECT domain ubiquitin ligase HUWE1 targets unassembled soluble proteins for degradation
por: Xu, Yue, et al.
Publicado: (2016)

Physics of scintillation in REA1O$_{3}:Ce^{3+}$ (RE=Y, Lu)
por: Korzhik, M V, et al.
Publicado: (2005)

Tracembler – software for in-silico chromosome walking in unassembled genomes
por: Dong, Qunfeng, et al.
Publicado: (2007)

SilkDB: a knowledgebase for silkworm biology and genomics
por: Wang, Jing, et al.
Publicado: (2005)

McClintock: An Integrated Pipeline for Detecting Transposable Element Insertions in Whole-Genome Shotgun Sequencing Data
por: Nelson, Michael G., et al.
Publicado: (2017)

Pan-arthropod analysis reveals somatic piRNAs as an ancestral defence against transposable elements
por: Lewis, Samuel H., et al.
Publicado: (2017)

Pathoscope: Species identification and strain attribution with unassembled sequencing data
por: Francis, Owen E., et al.
Publicado: (2013)

Crass: identification and reconstruction of CRISPR from unassembled metagenomic data
por: Skennerton, Connor T., et al.
Publicado: (2013)

Transposable Elements Re-Wire and Fine-Tune the Transcriptome
por: Cowley, Michael, et al.
Publicado: (2013)

Accessing the Variability of Multicopy Genes in Complex Genomes using Unassembled Next-Generation Sequencing Reads: The Case of Trypanosoma cruzi Multigene Families
por: Reis-Cunha, João Luís, et al.
Publicado: (2022)

Unassembled CD147 is an endogenous endoplasmic reticulum–associated degradation substrate
por: Tyler, Ryan E., et al.
Publicado: (2012)

Predicting the functional repertoire of an organism from unassembled RNA–seq data
por: Landesfeind, Manuel, et al.
Publicado: (2014)

Development of the Reading Cognitive Test Kyoto (ReaCT Kyoto) for Early Detection of Cognitive Decline in Patients with Hearing Loss
por: Okano, Takayuki, et al.
Publicado: (2020)

ChickVD: a sequence variation database for the chicken genome
por: Wang, Jing, et al.
Publicado: (2005)

Two-Photon Holographic Stimulation of ReaChR
por: Chaigneau, Emmanuelle, et al.
Publicado: (2016)

Assembled and unassembled pools of clathrin: a quantitative study using an enzyme immunoassay
Publicado: (1985)

A conserved quality-control pathway that mediates degradation of unassembled ribosomal proteins
por: Sung, Min-Kyung, et al.
Publicado: (2016)

MetaCRAST: reference-guided extraction of CRISPR spacers from unassembled metagenomes
por: Moller, Abraham G., et al.
Publicado: (2017)

Transposed-word effects when reading serially
por: Mirault, Jonathan, et al.
Publicado: (2022)

Evolution and Variation of the SARS-CoV Genome
por: Hu, Jianfei, et al.
Publicado: (2003)

Genome Organization of the SARS-CoV
por: Xu, Jing, et al.
Publicado: (2003)

Pigs in sequence space: A 0.66X coverage pig genome survey based on shotgun sequencing
por: Wernersson, Rasmus, et al.
Publicado: (2005)

Accurate Genome Relative Abundance Estimation Based on Shotgun Metagenomic Reads
por: Xia, Li C., et al.
Publicado: (2011)

Implications of Error-Prone Long-Read Whole-Genome Shotgun Sequencing on Characterizing Reference Microbiomes
por: Hu, Yu, et al.
Publicado: (2020)

Prolyl dihydroxylation of unassembled uS12/Rps23 regulates fungal hypoxic adaptation
por: Clasen, Sara J, et al.
Publicado: (2017)

Fast Diffusion of the Unassembled PetC1-GFP Protein in the Cyanobacterial Thylakoid Membrane
por: Kaňa, Radek, et al.
Publicado: (2020)

Structure and Dynamics of the Unassembled Nucleoprotein of Rabies Virus in Complex with Its Phosphoprotein Chaperone Module
por: Gérard, Francine C. A., et al.
Publicado: (2022)

Cannot write session to /tmp/vufind_sessions/sess_dp2keg8o5ljqm8f3ikptkmou5i