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[HTML][HTML] Retrotransposons in plant genomes: structure, identification, and classification through bioinformatics and machine learning
Transposable elements (TEs) are genomic units able to move within the genome of virtually
all organisms. Due to their natural repetitive numbers and their high structural diversity, the …
all organisms. Due to their natural repetitive numbers and their high structural diversity, the …
The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars
Coffea arabica, an allotetraploid hybrid of Coffea eugenioides and Coffea canephora, is the
source of approximately 60% of coffee products worldwide, and its cultivated accessions …
source of approximately 60% of coffee products worldwide, and its cultivated accessions …
The apricot (Prunus armeniaca L.) genome elucidates Rosaceae evolution and beta-carotenoid synthesis
F Jiang, J Zhang, S Wang, L Yang, Y Luo… - Horticulture …, 2019 - academic.oup.com
Apricots, scientifically known as Prunus armeniaca L, are drupes that resemble and are
closely related to peaches or plums. As one of the top consumed fruits, apricots are widely …
closely related to peaches or plums. As one of the top consumed fruits, apricots are widely …
A systematic review of the application of machine learning in the detection and classification of transposable elements
Background Transposable elements (TEs) constitute the most common repeated sequences
in eukaryotic genomes. Recent studies demonstrated their deep impact on species diversity …
in eukaryotic genomes. Recent studies demonstrated their deep impact on species diversity …
[HTML][HTML] Measuring performance metrics of machine learning algorithms for detecting and classifying transposable elements
Because of the promising results obtained by machine learning (ML) approaches in several
fields, every day is more common, the utilization of ML to solve problems in bioinformatics. In …
fields, every day is more common, the utilization of ML to solve problems in bioinformatics. In …
The absence of the caffeine synthase gene is involved in the naturally decaffeinated status of Coffea humblotiana, a wild species from Comoro archipelago
Caffeine is the most consumed alkaloid stimulant in the world. It is synthesized through the
activity of three known N-methyltransferase proteins. Here we are reporting on the 422-Mb …
activity of three known N-methyltransferase proteins. Here we are reporting on the 422-Mb …
Inpactor2: a software based on deep learning to identify and classify LTR-retrotransposons in plant genomes
S Orozco-Arias… - Briefings in …, 2023 - academic.oup.com
LTR-retrotransposons are the most abundant repeat sequences in plant genomes and play
an important role in evolution and biodiversity. Their characterization is of great importance …
an important role in evolution and biodiversity. Their characterization is of great importance …
InpactorDB: a classified lineage-level plant LTR retrotransposon reference library for free-alignment methods based on machine learning
S Orozco-Arias, PA Jaimes, MS Candamil… - Genes, 2021 - mdpi.com
Long terminal repeat (LTR) retrotransposons are mobile elements that constitute the major
fraction of most plant genomes. The identification and annotation of these elements via …
fraction of most plant genomes. The identification and annotation of these elements via …
LtrDetector: a tool-suite for detecting long terminal repeat retrotransposons de-novo
JD Valencia, HZ Girgis - BMC genomics, 2019 - Springer
Background Long terminal repeat retrotransposons are the most abundant transposons in
plants. They play important roles in alternative splicing, recombination, gene regulation, and …
plants. They play important roles in alternative splicing, recombination, gene regulation, and …
Tools and databases for solving problems in detection and identification of repetitive DNA sequences
Sažetak Genome compartments known to carry out very important biological functions (eg.
centromeres and telomeres) are mostly constituted of repetitive sequences. At the same …
centromeres and telomeres) are mostly constituted of repetitive sequences. At the same …