A survey of k-mer methods and applications in bioinformatics

A survey of k-mer methods and applications in bioinformatics

2024 | Camille Moeckel, Manvita Mareboina, Maxwell A. Kornaris, Candace S.Y. Chan, Ioannis Mouratidis, Austin Montgomery, Nikol Chantzi, Georgios A. Pavlopoulos, Ilias Georgakopoulos-Soares
This review summarizes the role and applications of k-mer methods in bioinformatics. K-mers are contiguous sequences of nucleotides or amino acids of fixed length, and they are widely used in genomic and proteomic data analysis. They offer computational efficiency and can have intrinsic biological significance. The review discusses the selection of k, the applications of k-mers, and the use of absent sequences such as nullomers and nullpeptides in disease detection, vaccine development, and therapeutics. K-mers are used in sequence alignment, genome assembly, error correction, genome editing, comparative genomics, metagenomics, metaproteomics, and protein structure modeling. The review also highlights the potential of absent sequences in identifying unique biomarkers, improving diagnostic accuracy, and developing targeted therapies. The use of k-mers in these applications has the potential to advance research and improve clinical outcomes.This review summarizes the role and applications of k-mer methods in bioinformatics. K-mers are contiguous sequences of nucleotides or amino acids of fixed length, and they are widely used in genomic and proteomic data analysis. They offer computational efficiency and can have intrinsic biological significance. The review discusses the selection of k, the applications of k-mers, and the use of absent sequences such as nullomers and nullpeptides in disease detection, vaccine development, and therapeutics. K-mers are used in sequence alignment, genome assembly, error correction, genome editing, comparative genomics, metagenomics, metaproteomics, and protein structure modeling. The review also highlights the potential of absent sequences in identifying unique biomarkers, improving diagnostic accuracy, and developing targeted therapies. The use of k-mers in these applications has the potential to advance research and improve clinical outcomes.
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