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

AI Article Synopsis

  • The reduction in sequencing costs has allowed scientists to develop reference genomes and proteomes for many organisms, but a comprehensive database for organism-specific genomic sequences (kmers) was lacking.
  • The article introduces kmerDB, a new database that organizes and provides access to kmer-based genomic and proteomic information using a user-friendly web interface.
  • kmerDB holds over 202 billion base pairs and nearly 19 billion amino acids from tens of thousands of reference genomes and proteomes, along with unique sequences not found in any genome or proteome.

Article 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.

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Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC11070822PMC
http://dx.doi.org/10.1016/j.csbj.2024.04.050DOI Listing

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