Detection and classification of long terminal repeat sequences in plant LTR-retrotransposons and their analysis using explainable machine learning [PDF]
BioData MiningBackground Long terminal repeats (LTRs) represent important parts of LTR retrotransposons and retroviruses found in high copy numbers in a majority of eukaryotic genomes.
Jakub Horvath +5 more
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Phylogenetic analysis of small ruminant lentiviruses originating from naturally infected sheep and goats from Poland based on the long terminal repeat sequences [PDF]
Journal of Veterinary Research, 2022 Previous gag and env sequence studies placed Polish small ruminant lentiviruses (SRLVs) isolated from sheep and goats in subtypes B1, B2, A1, A5, A12, A13, A16–A18, A23, A24 and A27.
Olech Monika +3 more
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Conserved presence of G-quadruplex forming sequences in the Long Terminal Repeat Promoter of Lentiviruses [PDF]
Scientific Reports, 2017 G-quadruplexes (G4s) are secondary structures of nucleic acids that epigenetically regulate cellular processes. In the human immunodeficiency lentivirus 1 (HIV-1), dynamic G4s are located in the unique viral LTR promoter.
Rosalba Perrone +3 more
doaj +2 more sources
Insertion Sequence Inversions Mediated by Ectopic Recombination between Terminal Inverted Repeats
PLoS ONE, 2010 Transposable elements are widely distributed and diverse in both eukaryotes and prokaryotes, as exemplified by DNA transposons. As a result, they represent a considerable source of genomic variation, for example through ectopic (i.e. non-allelic homologous) recombination events between transposable element copies, resulting in genomic rearrangements ...
Alison Ling, Richard Cordaux
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C-terminal low-complexity sequence repeats of Mycobacterium smegmatis Ku modulate DNA binding [PDF]
Bioscience Reports, 2012 Ku protein is an integral component of the NHEJ (non-homologous end-joining) pathway of DSB (double-strand break) repair. Both eukaryotic and prokaryotic Ku homologues have been characterized and shown to bind DNA ends. A unique feature of Mycobacterium smegmatis Ku is its basic C-terminal tail that contains several lysine-rich low-complexity PAKKA ...
Ambuj Kumar Kushwaha, Anne Grove
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Which factors contribute most to genome size variation within angiosperms?
Ecology and Evolution, 2021 Genome size varies greatly across the flowering plants and has played an important role in shaping their evolution. It has been reported that many factors correlate with the variation in genome size, but few studies have systematically explored this at ...
Dandan Wang +10 more
doaj +1 more source
Whole genome resequencing reveals natural target site preferences of transposable elements in Drosophila melanogaster. [PDF]
PLoS ONE, 2012 Transposable elements are mobile DNA sequences that integrate into host genomes using diverse mechanisms with varying degrees of target site specificity.
Raquel S Linheiro, Casey M Bergman
doaj +1 more source
Correction: Detection and classification of long terminal repeat sequences in plant LTR-retrotransposons and their analysis using explainable machine learning [PDF]
BioData MiningJakub Horvath +5 more
doaj +2 more sources
Hybrid Sequencing Resolved Inverted Terminal Repeats in the Genome of Megavirus Baoshan
Frontiers in Microbiology, 2022 Mimivirus is a group of amoeba-infecting DNA viruses with linear double-strand genome. It is found to be ubiquitous in nature worldwide. Here, we reported the complete genome of a new member of Mimivirus lineage C isolated from a fresh water pond in Shanghai, China. Its 1,224,839-bp genome encoded 1,062 predicted ORFs. Combining the results of Nanopore,
Yucheng Xia, Huanyu Cheng, Jiang Zhong
openaire +3 more sources
International Journal of Medical Microbiology, 2020 Mostly, blaCTX-M is found on transferable plasmids as a component of the blaCTX-M transposition unit containing an insertion sequence, ISEcp1, which exists on the upstream region of blaCTX-Ms.
Kouta Hamamoto +3 more
doaj +1 more source