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

Ioannis Mouratidis, Fotis A. Baltoumas, Nikol Chantzi, Michail Patsakis, Candace S.Y. Chan, Austin Montgomery, Maxwell A. Konnaris, Eleni Aplakidou, George C. Georgakopoulos, Anshuman Das, Dionysios V. Chartoumpekis, Jasna Kovac, Georgios A. Pavlopoulos, Ilias Georgakopoulos-Soares

Research output: Contribution to journalArticlepeer-review

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.

Original languageEnglish (US)
Pages (from-to)1919-1928
Number of pages10
JournalComputational and Structural Biotechnology Journal
Volume23
DOIs
StatePublished - Dec 2024

All Science Journal Classification (ASJC) codes

  • Biotechnology
  • Biophysics
  • Structural Biology
  • Biochemistry
  • Genetics
  • Computer Science Applications

Cite this