ArticleComputational and structural biotechnology journal2024
kmerDB: A database encompassing the set of genomic and proteomic sequence information for each species.
Article in Computational and structural biotechnology journal, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- Mass Spectrometry-Based Analysis of Surface Proteins inJournal of proteome research · 2025Article
- Taxonomic quasi-primes: peptides charting lineage-specific adaptations and disease-relevant loci.Protein science : a publication of the Protein Society · 2025Article
- Unraveling diversity by isolating peptide sequences specific to distinct taxonomic groups.bioRxiv : the preprint server for biology · 2025Article
- The topography of nullomer-emerging mutations and their relevance to human disease.Computational and structural biotechnology journal · 2025Article
- Investigating DNA words and their distributions across the tree of life.Computational and structural biotechnology journal · 2025Article
- A survey of k-mer methods and applications in bioinformatics.Computational and structural biotechnology journal · 2024Review
- The determinants of the rarity of nucleic and peptide short sequences in nature.NAR genomics and bioinformatics · 2024Article
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Authors and funding
14 authors.
Funding
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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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.