Results 41 to 50 of about 10,955,529 (276)
EURASIP Journal on Advances in Signal Processing, 2017 Background Diseases like cancer can manifest themselves through changes in protein abundance, and microRNAs (miRNAs) play a key role in the modulation of protein quantity.
Malik Yousef +4 more
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Recombination spot identification Based on gapped k-mers. [PDF]
Sci Rep, 2016 AbstractRecombination is crucial for biological evolution, which provides many new combinations of genetic diversity. Accurate identification of recombination spots is useful for DNA function study. To improve the prediction accuracy, researchers have proposed several computational methods for recombination spot identification.
Wang R, Xu Y, Liu B.
europepmc +3 more sources
Inter-chromosomal k-mer distances [PDF]
BMC Genomics, 2021 Abstract Background Inversion Symmetry is a generalization of the second Chargaff rule, stating that the count of a string of k nucleotides on a single chromosomal strand equals the count of its inverse (reverse-complement) k-mer.
Alon Kafri, Benny Chor, David Horn
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IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2023 Phylogenetically informed k-mers, or phylo-k-mers for short, are k-mers that are predicted to appear within a given genomic region at predefined locations of a fixed phylogeny. Given a reference alignment for this genomic region and assuming a phylogenetic model of sequence evolution, we can compute a probability score for any given k-mer at any given ...
Romashchenko, Nikolai +4 more
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Robust $$k$$ k -mer frequency estimation using gapped $$k$$ k -mers [PDF]
Journal of Mathematical Biology, 2013 Oligomers of fixed length, k, commonly known as k-mers, are often used as fundamental elements in the description of DNA sequence features of diverse biological function, or as intermediate elements in the constuction of more complex descriptors of sequence features such as position weight matrices.
Ghandi, Mahmoud +2 more
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Enhanced regulatory sequence prediction using gapped k-mer features. [PDF]
PLoS Computational Biology, 2014 Oligomers of length k, or k-mers, are convenient and widely used features for modeling the properties and functions of DNA and protein sequences. However, k-mers suffer from the inherent limitation that if the parameter k is increased to resolve longer ...
Mahmoud Ghandi +3 more
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Comparative analysis of DNA word abundances in four yeast genomes using a novel statistical background model. [PDF]
PLoS ONE, 2013 Previous studies have shown that the identification and analysis of both abundant and rare k-mers or "DNA words of length k" in genomic sequences using suitable statistical background models can reveal biologically significant sequence elements.
Ramkumar Hariharan +3 more
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Frontiers in Genetics, 2021 The exponential growth of genome sequences available has spurred research on pattern detection with the aim of extracting evolutionary signal. Traditional approaches, such as multiple sequence alignment, rely on positional homology in order to ...
Nikolaos Pechlivanis +6 more
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TahcoRoll: fast genomic signature profiling via thinned automaton and rolling hash
Medical Review, 2021 Genomic signatures like k-mers have become one of the most prominent approaches to describe genomic data. As a result, myriad real-world applications, such as the construction of de Bruijn graphs in genome assembly, have been benefited by recognizing ...
Ju Chelsea J.-T. +4 more
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Determining population structure from k-mer frequencies
Proceedings of the 13th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics, 2022 Abstract Background: Understanding population structure within species provides information on connections among different populations and how they evolve over time. This knowledge is important for studies ranging from evolutionary biology to large-scale variant-trait association studies.
Yana Hrytsenko +2 more
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