Measuring the Invisible: The Sequences Causal of Genome Size Differences in Eyebrights (Euphrasia) Revealed by k-mers. [PDF]
Front Plant Sci, 2022 Genome size variation within plant taxa is due to presence/absence variation, which may affect low-copy sequences or genomic repeats of various frequency classes.
Becher H, Sampson J, Twyford AD.
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Disk compression of k-mer sets [PDF]
Algorithms for Molecular Biology, 2021 AbstractK-mer based methods have become prevalent in many areas of bioinformatics. In applications such as database search, they often work with large multi-terabyte-sized datasets. Storing such large datasets is a detriment to tool developers, tool users, and reproducibility efforts.
Amatur Rahman +2 more
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KEC: unique sequence search by K-mer exclusion [PDF]
Bioinformatics, 2021 Abstract Summary Searching for amino acid or nucleic acid sequences unique to one organism may be challenging depending on size of the available datasets. K-mer elimination by cross-reference (KEC) allows users to quickly and easily find unique sequences by providing target and non-target sequences ...
Pavel Beran +3 more
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Efficient counting of
BMC Bioinformatics, 2011 Background Counting k-mers (substrings of length k in DNA sequence data) is an essential component of many methods in bioinformatics, including for genome and transcriptome assembly, for metagenomic sequencing, and for error correction of sequence reads.
Melsted Páll, Pritchard Jonathan K
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The Statistics of <i>k</i>-mers from a Sequence Undergoing a Simple Mutation Process Without Spurious Matches. [PDF]
J Comput Biol, 2022 k-mer-based methods are widely used in bioinformatics, but there are many gaps in our understanding of their statistical properties. Here, we consider the simple model where a sequence S (e.g., a genome or a read) undergoes a simple mutation process ...
Blanca A +3 more
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Unraveling Plant Recombination Patterns: Insights From Genome k‐mers [PDF]
Plant DirectCrossover recombination is a pivotal event that takes place during meiosis of germinal cells, leading to the rearrangement of parental chromosomes and generating novel allele combinations, thereby enhancing genetic diversity.
Mauricio Peñuela +3 more
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Measuring Genome Sizes Using Read-Depth, k-mers, and Flow Cytometry: Methodological Comparisons in Beetles (Coleoptera). [PDF]
G3 (Bethesda), 2020 Measuring genome size across different species can yield important insights into evolution of the genome and allow for more informed decisions when designing next-generation genomic sequencing projects.
Pflug JM +4 more
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bioRxivWe introduce a pseudoassembly approach to identifying variation in sets of genomic sequences via colored de Bruijn graphs. Our pseudoassembly method is implemented in a program called klue that assembles k-mers into sequences compatible with a variant ...
Delaney K. Sullivan +2 more
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Phylogenetic Analysis of HIV-1 Genomes Based on the Position-Weighted K-mers Method. [PDF]
Entropy (Basel), 2020 HIV-1 viruses, which are predominant in the family of HIV viruses, have strong pathogenicity and infectivity. They can evolve into many different variants in a very short time.
Ma Y +5 more
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Reference-free Association Mapping from Sequencing Reads Using k-mers [PDF]
Bio-Protocol, 2020 Association mapping is the process of linking phenotypes with genotypes. In genome wide association studies (GWAS), individuals are first genotyped using microarrays or by aligning sequenced reads to reference genomes. However, both these approaches rely
Zakaria Mehrab +4 more
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