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Kegg: biological systems database as a model of the real world.

Last updated at Posted at 2025-08-05

Kegg: biological systems database as a model of the real world.

M. Kanehisa, M. Furumichi, Y. Sato, Y. Matsuura, and M. Ishiguro-Watanabe. Nucleic Acids Research, 53:D672–D677, 1 2025. ISSN 0305-1048. doi: 10.1093/NAR/GKAE909. URL https://dx.doi.org/10.1093/nar/gkae909.

References

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  2. Kanehisa,M.,Furumichi,M.,Sato,Y.,Kawashima,M.and Ishiguro-Watanabe,M.(2023) KEGG for taxonomy-based analysis of pathways and genomes.Nucleic Acids Res.,51,D587–D592.
  3. Jin,Z.,Sato,Y.,Kawashima,M.and Kanehisa,M.(2023) KEGG tools for classification and analysis of viral proteins.Protein Sci., 32,e4840.
  4. Fujibuchi,W.,Goto,S.,Migimatsu,H.,Uchiyama,I.,Ogiwara,A., Akiyama,Y.and Kanehisa,M.(1998) DBGET/LinkDB: an integrated database retrieval system.Pac. Symp. Biocomput., 683–694.
  5. Kanehisa,M.and Sato,Y.(2020) KEGG Mapper for inferring cellular functions from protein sequences.Protein Sci.,29,28–35.
  6. Kanehisa,M.,Sato,Y.and Kawashima,M.(2022) KEGG mapping tools for uncovering hidden features in biological data.Protein Sci.,31,47–53.
  7. Haft,D.H.,Badretdin,A.,Coulouris,G.,DiCuccio,M.,Durkin,A.S., Jovenitti,E.,Li,W.,Mersha,M.,O’Neill,K.R.,Virothaisakun,J.,et al. (2024) RefSeq and the prokaryotic genome annotation pipeline in the age of metagenomes.Nucleic Acids Res.,52,D762–D769.
  8. Goad,W.B.and Kanehisa,M.I.(1982) Pattern recognition in nucleic acid sequences.I.A general method for finding local homologies and symmetries.Nucleic Acids Res.,10,247–263.
  9. Smith,T.F.and Waterman,M.S.(1981) Identification of common molecular subsequences.J. Mol. Biol.,147,195–197.
  10. Schoch,C.L.,Ciufo,S.,Domrachev,M.,Hotton,C.L.,Kannan,S., Khovanskaya, R.,Leipe, D.,Mcveigh, R.,O’Neill,K.,Robbertse,B., et al. (2020) NCBI Taxonomy: a comprehensive update on curation,resources and tools.Database,2020,baaa062.
  11. Siddell,S.G.,Smith,D.B.,Adriaenssens,E.,Alfenas-Zerbini,P., Dutilh, B.E.,Garcia, M.L.,Junglen, S.,Krupovic, M.,Kuhn, J.H., Lambert,A.J.,et al. (2023) Virus taxonomy and the role of the International Committee on Taxonomy of Viruses (ICTV).J. Gen. Virol.,104,001840.

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