scholarly journals MGEScan-non-LTR: computational identification and classification of autonomous non-LTR retrotransposons in eukaryotic genomes

2009 ◽  
Vol 37 (21) ◽  
pp. e143-e143 ◽  
Author(s):  
M. Rho ◽  
H. Tang
Keyword(s):  
Ltr Retrotransposons ◽  
Computational Identification ◽  
Eukaryotic Genomes

scholarly journals TEsorter: lineage-level classification of transposable elements using conserved protein domains

2019 ◽  
Author(s):  
Ren-Gang Zhang ◽  
Zhao-Xuan Wang ◽  
Shujun Ou ◽  
Guang-Yuan Li
Keyword(s):  
Transposable Elements ◽  
Phylogenetic Relationships ◽  
Protein Domains ◽  
Ltr Retrotransposons ◽  
Link Type ◽  
Eukaryotic Genomes

AbstractSummaryTransposable elements (TEs) constitute an import part in eukaryotic genomes, but their classification, especially in the lineage or clade level, is still challenging. For this purpose, we propose TEsorter, which is based on conserved protein domains of TEs. It is easy-to-use, fast with multiprocessing, sensitive and precise to classify TEs especially LTR retrotransposons (LTR-RTs). Its results can also directly reflect phylogenetic relationships and diversities of the classified LTR-RTs.AvailabilityThe code in Python is freely available at https://github.com/zhangrengang/TEsorter.

scholarly journals Conversion of DNA Sequences: From a Transposable Element to a Tandem Repeat or to a Gene

Genes ◽  
2019 ◽  
Vol 10 (12) ◽  
pp. 1014 ◽  
Author(s):  
Ana Paço ◽  
Renata Freitas ◽  
Ana Vieira-da-Silva
Keyword(s):  
Repetitive Dna ◽  
Dna Sequences ◽  
Tandem Repeats ◽  
Evolutionary Relationship ◽  
Repetitive Dna Sequences ◽  
Dna Remodeling ◽  
Eukaryotic Genomes ◽  
Similar Organization ◽  
Dispersed Repeats

Eukaryotic genomes are rich in repetitive DNA sequences grouped in two classes regarding their genomic organization: tandem repeats and dispersed repeats. In tandem repeats, copies of a short DNA sequence are positioned one after another within the genome, while in dispersed repeats, these copies are randomly distributed. In this review we provide evidence that both tandem and dispersed repeats can have a similar organization, which leads us to suggest an update to their classification based on the sequence features, concretely regarding the presence or absence of retrotransposons/transposon specific domains. In addition, we analyze several studies that show that a repetitive element can be remodeled into repetitive non-coding or coding sequences, suggesting (1) an evolutionary relationship among DNA sequences, and (2) that the evolution of the genomes involved frequent repetitive sequence reshuffling, a process that we have designated as a “DNA remodeling mechanism”. The alternative classification of the repetitive DNA sequences here proposed will provide a novel theoretical framework that recognizes the importance of DNA remodeling for the evolution and plasticity of eukaryotic genomes.

scholarly journals DeepTE: a computational method for de novo classification of transposons with convolutional neural network

2020 ◽  
Author(s):  
Haidong Yan ◽  
Aureliano Bombarely ◽  
Song Li
Keyword(s):  
Neural Network ◽  
Convolutional Neural Network ◽  
De Novo ◽  
Genomic Sequence ◽  
Computational Method ◽  
Model Species ◽  
Essential Step ◽  
Genomic Sequence Analysis ◽  
Eukaryotic Genomes

AbstractMotivationTransposable elements (TEs) classification is an essential step to decode their roles in genome evolution. With a large number of genomes from non-model species becoming available, accurate and efficient TE classification has emerged as a new challenge in genomic sequence analysis.ResultsWe developed a novel tool, DeepTE, which classifies unknown TEs using convolutional neural networks. DeepTE transferred sequences into input vectors based on k-mer counts. A tree structured classification process was used where eight models were trained to classify TEs into super families and orders. DeepTE also detected domains inside TEs to correct false classification. An additional model was trained to distinguish between non-TEs and TEs in plants. Given unclassified TEs of different species, DeepTE can classify TEs into seven orders, which include 15, 24, and 16 super families in plants, metazoans, and fungi, respectively. In several benchmarking tests, DeepTE outperformed other existing tools for TE classification. In conclusion, DeepTE successfully leverages convolutional neural network for TE classification, and can be used to precisely identify and annotate TEs in newly sequenced eukaryotic genomes.AvailabilityDeepTE is accessible at https://github.com/LiLabAtVT/[email protected]

scholarly journals De novo identification of LTR retrotransposons in eukaryotic genomes

BMC Genomics ◽  
2007 ◽  
Vol 8 (1) ◽  
pp. 90 ◽  
Author(s):  
Mina Rho ◽  
Jeong-Hyeon Choi ◽  
Sun Kim ◽  
Michael Lynch ◽  
Haixu Tang
Keyword(s):  
De Novo ◽  
Ltr Retrotransposons ◽  
Eukaryotic Genomes

Computational approaches for identification and classification of transposable elements in eukaryotic genomes

2012 ◽  
Vol 34 (8) ◽  
pp. 1009-1019
Author(s):  
Hong-En XU ◽  
Hua-Hao ZHANG ◽  
Min-Jin HAN ◽  
Yi-Hong SHEN ◽  
Xian-Zhi HUANG ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Computational Approaches ◽  
Eukaryotic Genomes

scholarly journals Fine-grained annotation and classification of de novo predicted LTR retrotransposons

2009 ◽  
Vol 37 (21) ◽  
pp. 7002-7013 ◽  
Author(s):  
Sascha Steinbiss ◽  
Ute Willhoeft ◽  
Gordon Gremme ◽  
Stefan Kurtz
Keyword(s):  
De Novo ◽  
Ltr Retrotransposons ◽  
Fine Grained

scholarly journals Simple and fast classification of non-LTR retrotransposons based on phylogeny of their RT domain protein sequences

Gene ◽  
2009 ◽  
Vol 448 (2) ◽  
pp. 207-213 ◽  
Author(s):  
Vladimir V. Kapitonov ◽  
Sébastien Tempel ◽  
Jerzy Jurka
Keyword(s):  
Protein Sequences ◽  
Ltr Retrotransposons ◽  
Domain Protein ◽  
Fast Classification
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