Results 11 to 20 of about 10,955,529 (276)
MicroRNA categorization using sequence motifs and k-mers. [PDF]
BMC Bioinformatics, 2017 Post-transcriptional gene dysregulation can be a hallmark of diseases like cancer and microRNAs (miRNAs) play a key role in the modulation of translation efficiency.
Yousef M, Khalifa W, Acar İE, Allmer J.
europepmc +7 more sources
CoMeta: classification of metagenomes using k-mers. [PDF]
PLoS ONE, 2015 Nowadays, the study of environmental samples has been developing rapidly. Characterization of the environment composition broadens the knowledge about the relationship between species composition and environmental conditions.
Jolanta Kawulok, Sebastian Deorowicz
doaj +6 more sources
EPIK: precise and scalable evolutionary placement with informative k-mers. [PDF]
Bioinformatics, 2023 Motivation Phylogenetic placement enables phylogenetic analysis of massive collections of newly sequenced DNA, when de novo tree inference is too unreliable or inefficient. Assuming that a high-quality reference tree is available, the idea is to seek the
Romashchenko N +3 more
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Plasmer: an Accurate and Sensitive Bacterial Plasmid Prediction Tool Based on Machine Learning of Shared k-mers and Genomic Features. [PDF]
Microbiol Spectr, 2023 In this study, we proposed a novel plasmid prediction tool named Plasmer. Technically, unlike existing k-mer or genomic features-based methods, Plasmer is the first tool to combine the advantages of the percent of shared k-mers and the alignment score of
Zhu Q, Gao S, Xiao B, He Z, Hu S.
europepmc +2 more sources
Locality-preserving minimal perfect hashing of k-mers. [PDF]
Bioinformatics, 2023 Motivation Minimal perfect hashing is the problem of mapping a static set of n distinct keys into the address space {1,…,n} bijectively. It is well-known that n log 2(e) bits are necessary to specify a minimal perfect hash function (MPHF) f, when no ...
Pibiri GE, Shibuya Y, Limasset A.
europepmc +3 more sources
Phenetic Comparison of Prokaryotic Genomes Using k-mers. [PDF]
Mol Biol Evol, 2017 Bacterial genomics studies are getting more extensive and complex, requiring new ways to envision analyses. Using the Ray Surveyor software, we demonstrate that comparison of genomes based on their k-mer content allows reconstruction of phenetic trees ...
Déraspe M +6 more
europepmc +5 more sources
General encoding of canonical k-mers
Peer Community Journal, 2023 To index or compare sequences efficiently, often k-mers, i.e., substrings of fixed length k, are used. For efficient indexing or storage, k-mers are often encoded as integers, e.g., applying some bijective mapping between all possible σk k-mers and the ...
Wittler, Roland
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On weighted k-mer dictionaries
Algorithms for Molecular Biology, 2023 We consider the problem of representing a set of $$k$$ k -mers and their abundance counts, or weights, in compressed space so that assessing membership and retrieving the weight of a $$k$$ k -mer is efficient.
Giulio Ermanno Pibiri
doaj +9 more sources
Flexible protein database based on amino acid k-mers. [PDF]
Sci Rep, 2022 Identification of proteins is one of the most computationally intensive steps in genomics studies. It usually relies on aligners that do not accommodate rich information on proteins and require additional pipelining steps for protein identification.
Déraspe M +4 more
europepmc +2 more sources
SAKE: Strobemer-assisted k-mer extraction.
PLoS ONE, 2023 K-mer-based analysis plays an important role in many bioinformatics applications, such as de novo assembly, sequencing error correction, and genotyping.
Miika Leinonen, Leena Salmela
doaj +5 more sources