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searching for K-mer 18 found (41 total)

alternate case: k-mer

Alignment-free sequence analysis (6,323 words) [view diff] exact match in snippet view article find links to article

each possible k-mer (possible number of k-mers for nucleotide sequence: 4k, while that for protein sequence: 20k) in sequences. Each k-mer count in each

BLAT (bioinformatics) (2,168 words) [view diff] exact match in snippet view article

sequences i.e. the two k-mer words are exactly the same. This approach is not considered the most practical. This is because a small k-mer size is necessary

Functional genomics (3,724 words) [view diff] exact match in snippet view article find links to article

have required machine learning approaches to interpret the data. A gapped k-mer SVM model has been used to infer the kmers that are enriched within cis-regulatory

Eugene Myers (584 words) [view diff] exact match in snippet view article find links to article

Retrieved 12 October 2012. Twitter feed "GitHub - thegenemyers/FASTK: A fast K-mer counter for high-fidelity shotgun datasets". GitHub. Retrieved 2021-08-27

Planted motif search (4,694 words) [view diff] exact match in snippet view article find links to article

position ij such that a k-mer of Q occurs starting from ij. Another k-mer of Q occurs starting from ij +1 and so on, with the last k-mer occurring at ij + l

Cardiobacterium hominis (1,941 words) [view diff] exact match in snippet view article find links to article

disregarded. Assembly was performed by SPAdes genome assembler using different k-mer values from 43-127 and Quast using N50 and L50 scores and the lowest quantity

Rooibos (3,428 words) [view diff] case mismatch in snippet view article find links to article

"Rooibos (Aspalathus linearis) genome size estimation using flow cytometry and K-Mer analyses". Plants. 9 (2): 270. doi:10.3390/plants9020270. PMC 7076435. PMID 32085566

List of sequence alignment software (2,355 words) [view diff] exact match in snippet view article find links to article

reads using a banded Smith-Waterman algorithm seeded by results from a k-mer hashing scheme. Supports reads ranging in size from very short to very long

Pomatoceros lamarckii (303 words) [view diff] exact match in snippet view article find links to article

PMID 19781084. Kenny, Nathan J; Shimeld, Sebastian M (2012). "Additive multiple k-mer transcriptome of the keelworm Pomatoceros lamarckii (Annelida; Serpulidae)

Getah virus (543 words) [view diff] exact match in snippet view article find links to article

Warrilow D, Tang B; et al. (2020). "Sequencing of Historical Isolates, K-mer Mining and High Serological Cross-Reactivity with Ross River Virus Argue

Protein fragment library (1,295 words) [view diff] exact match in snippet view article find links to article

derived using only samples found in the PDB with the same sequence in the k-mer fragment. This requires more computational work than deriving a sequence-independent

David Horn (Israeli physicist) (1,976 words) [view diff] exact match in snippet view article

Chor, David Horn, Yaron Levy, Nick Goldman and Tim Massingham: Genomic DNA k-mer spectra: models and modalities. Genome Biology 2009, 10(10):R108 Erez Persi

Marine viruses (9,231 words) [view diff] exact match in snippet view article find links to article

Ahlgren NA, Lu YY, Fuhrman JA, Sun F (July 2017). "VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data"

MG-RAST (980 words) [view diff] exact match in snippet view article find links to article

FASTQ data dereplication Dereplication for shotgun metagenome data by using k-mer approach screen Removing reads that are near-exact matches to the genomes

List of RNA-Seq bioinformatics tools (20,462 words) [view diff] exact match in snippet view article find links to article

sequencing reads. Blue Blue is a short-read error-correction tool based on k-mer consensus and context. BFC A sequencing error corrector designed for Illumina

Hybrid genome assembly (2,951 words) [view diff] exact match in snippet view article find links to article

approach, the length of the assembled sequences does not matter as once a k-mer spectrum has been constructed, the lengths of the reads are irrelevant.

List of RNA structure prediction software (8,423 words) [view diff] exact match in snippet view article find links to article

integrated framework for piRNA prediction employing hybrid features like k-mer nucleotide composition, secondary structure, thermodynamic and physicochemical

Genome skimming (4,505 words) [view diff] exact match in snippet view article find links to article

uses a 2 stage approach to compute these distances. First, it generates k-mer frequency profiling using a tool called JellyFish and then these k-mers