kmerDB

kmerDB provides a species-indexed collection of fixed-length nucleotide and amino-acid sequences (kmers) for comparative genomic and proteomic analyses.

Key Features:

• Extensive data coverage: The database encompasses 202,340,859,107 base pairs across 54,039 reference genomes and 19,304,903,356 amino acids across 21,865 proteomes.
• Quasi-primes (species-specific sequences): Includes 6,905,362 genomic and 149,305,183 proteomic species-specific sequences termed quasi-primes.
• Primes (absent sequences): Provides 5,186,757 nucleic and 214,904,089 peptide sequences that are absent from every genome and proteome, referred to as primes.
• Kmer-based indexing: Organizes genomic and proteomic sequences by specific kmer lengths for sequence-level analysis and retrieval.

Scientific Applications:

• Comparative genomics: Enables comparison of fixed-length nucleotide kmers across 54,039 reference genomes for species- and strain-level analyses.
• Evolutionary biology: Supports analyses of kmer conservation and divergence across genomes and proteomes to infer evolutionary relationships.
• Functional genomics: Facilitates identification of peptide kmers and sequence motifs across 21,865 proteomes for functional inference.
• Unique-sequence characterization: Allows investigation of quasi-primes and primes to study species-specific and universally absent sequence features.

Methodology:

Sequences are organized and indexed by specific kmer lengths to provide a structured approach to data retrieval and analysis.