kmerDB: A database encompassing the set of genomic and proteomic sequence information for each species.

Autor:	Mouratidis I; Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA.; Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA., Baltoumas FA; Institute for Fundamental Biomedical Research, BSRC 'Alexander Fleming', Vari, 16672, Greece., Chantzi N; Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA., Patsakis M; Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA., Chan CSY; Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA., Montgomery A; Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA., Konnaris MA; Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA.; Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA.; Department of Statistics, The Pennsylvania State University, University Park, PA, USA., Aplakidou E; Institute for Fundamental Biomedical Research, BSRC 'Alexander Fleming', Vari, 16672, Greece.; Department of Basic Sciences, School of Medicine, University of Crete, Heraklion, Greece., Georgakopoulos GC; National Technical University of Athens, School of Electrical and Computer Engineering, Athens, Greece., Das A; Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA., Chartoumpekis DV; Service of Endocrinology, Diabetology and Metabolism, Lausanne University Hospital, Lausanne, Switzerland., Kovac J; Department of Food Science, The Pennsylvania State University, University Park, PA 16802, USA., Pavlopoulos GA; Institute for Fundamental Biomedical Research, BSRC 'Alexander Fleming', Vari, 16672, Greece.; Center for New Biotechnologies and Precision Medicine, School of Medicine, National and Kapodistrian University of Athens, Athens, 11527, Greece., Georgakopoulos-Soares I; Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA.
Jazyk:	angličtina
Zdroj:	Computational and structural biotechnology journal [Comput Struct Biotechnol J] 2024 Apr 21; Vol. 23, pp. 1919-1928. Date of Electronic Publication: 2024 Apr 21 (Print Publication: 2024).
DOI:	10.1016/j.csbj.2024.04.050
Abstrakt:	The decrease in sequencing expenses has facilitated the creation of reference genomes and proteomes for an expanding array of organisms. Nevertheless, no established repository that details organism-specific genomic and proteomic sequences of specific lengths, referred to as kmers, exists to our knowledge. In this article, we present kmerDB, a database accessible through an interactive web interface that provides kmer-based information from genomic and proteomic sequences in a systematic way. kmerDB currently contains 202,340,859,107 base pairs and 19,304,903,356 amino acids, spanning 54,039 and 21,865 reference genomes and proteomes, respectively, as well as 6,905,362 and 149,305,183 genomic and proteomic species-specific sequences, termed quasi-primes. Additionally, we provide access to 5,186,757 nucleic and 214,904,089 peptide sequences absent from every genome and proteome, termed primes. kmerDB features a user-friendly interface offering various search options and filters for easy parsing and searching. The service is available at: www.kmerdb.com. Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. (© 2024 The Authors.)
Databáze:	MEDLINE
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