MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets - PubMed (original) (raw)

. 2017 Nov;35(11):1026-1028.

doi: 10.1038/nbt.3988. Epub 2017 Oct 16.

Affiliations

• PMID: 29035372
• DOI: 10.1038/nbt.3988

MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets

Martin Steinegger et al. Nat Biotechnol. 2017 Nov.

No abstract available

PubMed Disclaimer

Similar articles

• pFind: a novel database-searching software system for automated peptide and protein identification via tandem mass spectrometry.
  Li D, Fu Y, Sun R, Ling CX, Wei Y, Zhou H, Zeng R, Yang Q, He S, Gao W. Li D, et al. Bioinformatics. 2005 Jul 1;21(13):3049-50. doi: 10.1093/bioinformatics/bti439. Epub 2005 Apr 7. Bioinformatics. 2005. PMID: 15817687
• Sequence Similarity Searching.
  Hu G, Kurgan L. Hu G, et al. Curr Protoc Protein Sci. 2019 Feb;95(1):e71. doi: 10.1002/cpps.71. Epub 2018 Aug 13. Curr Protoc Protein Sci. 2019. PMID: 30102464 Review.
• MagicMatch--cross-referencing sequence identifiers across databases.
  Smith M, Kunin V, Goldovsky L, Enright AJ, Ouzounis CA. Smith M, et al. Bioinformatics. 2005 Aug 15;21(16):3429-30. doi: 10.1093/bioinformatics/bti548. Epub 2005 Jun 16. Bioinformatics. 2005. PMID: 15961438
• Using relational databases for improved sequence similarity searching and large-scale genomic analyses.
  Mackey AJ, Pearson WR. Mackey AJ, et al. Curr Protoc Bioinformatics. 2004 Oct;Chapter 9:Unit 9.4. doi: 10.1002/0471250953.bi0904s7. Curr Protoc Bioinformatics. 2004. PMID: 18428739
• Large-scale database searching using tandem mass spectra: looking up the answer in the back of the book.
  Sadygov RG, Cociorva D, Yates JR 3rd. Sadygov RG, et al. Nat Methods. 2004 Dec;1(3):195-202. doi: 10.1038/nmeth725. Nat Methods. 2004. PMID: 15789030 Review.

Cited by

• Microbial species and intraspecies units exist and are maintained by ecological cohesiveness coupled to high homologous recombination.
  Conrad RE, Brink CE, Viver T, Rodriguez-R LM, Aldeguer-Riquelme B, Hatt JK, Venter SN, Rossello-Mora R, Amann R, Konstantinidis KT. Conrad RE, et al. Nat Commun. 2024 Nov 15;15(1):9906. doi: 10.1038/s41467-024-53787-0. Nat Commun. 2024. PMID: 39548060 Free PMC article.
• Integrated virtual screening and MD simulation study to discover potential inhibitors of mycobacterial electron transfer flavoprotein oxidoreductase.
  Arshad K, Salim J, Talat MA, Ashraf A, Kanwal N. Arshad K, et al. PLoS One. 2024 Nov 15;19(11):e0312860. doi: 10.1371/journal.pone.0312860. eCollection 2024. PLoS One. 2024. PMID: 39546486 Free PMC article.
• Ubiquitous genome streamlined Acidobacteriota in freshwater environments.
  Wong HL, Bulzu PA, Ghai R, Chiriac MC, Salcher MM. Wong HL, et al. ISME Commun. 2024 Oct 22;4(1):ycae124. doi: 10.1093/ismeco/ycae124. eCollection 2024 Jan. ISME Commun. 2024. PMID: 39544963 Free PMC article.
• Diversification of molecular pattern recognition in bacterial NLR-like proteins.
  Béchon N, Tal N, Stokar-Avihail A, Savidor A, Kupervaser M, Melamed S, Amitai G, Sorek R. Béchon N, et al. Nat Commun. 2024 Nov 14;15(1):9860. doi: 10.1038/s41467-024-54214-0. Nat Commun. 2024. PMID: 39543107 Free PMC article.
• Missing microbial eukaryotes and misleading meta-omic conclusions.
  Krinos AI, Mars Brisbin M, Hu SK, Cohen NR, Rynearson TA, Follows MJ, Schulz F, Alexander H. Krinos AI, et al. Nat Commun. 2024 Nov 14;15(1):9873. doi: 10.1038/s41467-024-52212-w. Nat Commun. 2024. PMID: 39543100 Free PMC article.

References

1. 1. Cell Syst. 2015 Jul 29;1(1):72-87 - PubMed
2. 1. Nucleic Acids Res. 2011 Mar;39(4):e23 - PubMed
3. 1. BMC Bioinformatics. 2011 Jun 01;12:221 - PubMed
4. 1. Nat Rev Microbiol. 2015 Jun;13(6):360-72 - PubMed
5. 1. PLoS One. 2013;8(2):e57355 - PubMed

Publication types

MeSH terms

LinkOut - more resources

• Full Text Sources

  • Nature Publishing Group

• Other Literature Sources

  • The Lens - Patent Citations Database
  • scite Smart Citations