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

Details

Serval ID
serval:BIB_00E21235BAF6
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
kmerDB: A database encompassing the set of genomic and proteomic sequence information for each species.
Journal
Computational and structural biotechnology journal
Author(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
Publication state
Published
Issued date
12/2024
Peer-reviewed
Oui
Volume
23
Pages
1919-1928
Language
english
Notes
Publication types: Journal Article
Publication Status: epublish
Abstract
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.
Keywords
Genome, K-mer, Nullomer, Prime, Proteome, Quasi-prime
Pubmed
Open Access
Yes
Create date
10/05/2024 15:46
Last modification date
11/05/2024 8:43
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