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

Détails

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Etat: Public
Version: Final published version
Licence: CC BY-NC-ND 4.0
ID Serval
serval:BIB_00E21235BAF6
Type
Article: article d'un périodique ou d'un magazine.
Collection
Publications
Institution
Titre
kmerDB: A database encompassing the set of genomic and proteomic sequence information for each species.
Périodique
Computational and structural biotechnology journal
Auteur⸱e⸱s
Mouratidis I., Baltoumas F.A., Chantzi N., Patsakis M., Chan CSY, Montgomery A., Konnaris M.A., Aplakidou E., Georgakopoulos G.C., Das A., Chartoumpekis D.V., Kovac J., Pavlopoulos G.A., Georgakopoulos-Soares I.
ISSN
2001-0370 (Print)
ISSN-L
2001-0370
Statut éditorial
Publié
Date de publication
12/2024
Peer-reviewed
Oui
Volume
23
Pages
1919-1928
Langue
anglais
Notes
Publication types: Journal Article
Publication Status: epublish
Résumé
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.
Mots-clé
Genome, K-mer, Nullomer, Prime, Proteome, Quasi-prime
Pubmed
Web of science
Open Access
Oui
Création de la notice
10/05/2024 14:46
Dernière modification de la notice
09/08/2024 14:55
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