kmerDB: A Database Encompassing the Set of Genomic and Proteomic Sequence Information for Each Species

Abstract

ABSTRACTThe rapid decline in sequencing cost has enabled the generation of reference genomes and proteomes for a growing number of organisms. However, at the present time, there is no established repository that provides information about organism-specific genomic and proteomic sequences of certain lengths, also known as kmers, that are either present or absent in each genome or proteome. 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 45,785 and 22,386 reference genomes and proteomes, respectively, as well as 14,658,776 and 149,264,442 genomic and proteomic species-specific sequences, termed quasi-primes. Additionally, we provide access to 5,186,757 nucleic and 214,904,089 peptide sequences that are 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.