Accurately clustering biological sequences in linear time by relatedness sorting
Author
Abstract
Suggested Citation
DOI: 10.1038/s41467-024-47371-9
Download full text from publisher
References listed on IDEAS
- Caroline M Weisman & Andrew W Murray & Sean R Eddy, 2020. "Many, but not all, lineage-specific genes can be explained by homology detection failure," PLOS Biology, Public Library of Science, vol. 18(11), pages 1-24, November.
- Yunpeng Cai & Wei Zheng & Jin Yao & Yujie Yang & Volker Mai & Qi Mao & Yijun Sun, 2017. "ESPRIT-Forest: Parallel clustering of massive amplicon sequence data in subquadratic time," PLOS Computational Biology, Public Library of Science, vol. 13(4), pages 1-16, April.
- Martin Steinegger & Johannes Söding, 2018. "Clustering huge protein sequence sets in linear time," Nature Communications, Nature, vol. 9(1), pages 1-8, December.
- Inigo Barrio-Hernandez & Jingi Yeo & Jürgen Jänes & Milot Mirdita & Cameron L. M. Gilchrist & Tanita Wein & Mihaly Varadi & Sameer Velankar & Pedro Beltrao & Martin Steinegger, 2023. "Clustering predicted structures at the scale of the known protein universe," Nature, Nature, vol. 622(7983), pages 637-645, October.
Most related items
These are the items that most often cite the same works as this one and are cited by the same works as this one.- Junhui Peng & Li Zhao, 2024. "The origin and structural evolution of de novo genes in Drosophila," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
- Mindaugas Margelevičius, 2024. "GTalign: spatial index-driven protein structure alignment, superposition, and search," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
- Peicong Lin & Yumeng Yan & Huanyu Tao & Sheng-You Huang, 2023. "Deep transfer learning for inter-chain contact predictions of transmembrane protein complexes," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
- Rubén Barcia-Cruz & David Goudenège & Jorge A. Moura de Sousa & Damien Piel & Martial Marbouty & Eduardo P. C. Rocha & Frédérique Roux, 2024. "Phage-inducible chromosomal minimalist islands (PICMIs), a novel family of small marine satellites of virulent phages," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
- Pedro Patraquim & Emile G. Magny & José I. Pueyo & Ana Isabel Platero & Juan Pablo Couso, 2022. "Translation and natural selection of micropeptides from long non-canonical RNAs," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
- Yiqian Duan & Célio Dias Santos-Júnior & Thomas Sebastian Schmidt & Anthony Fullam & Breno L. S. Almeida & Chengkai Zhu & Michael Kuhn & Xing-Ming Zhao & Peer Bork & Luis Pedro Coelho, 2024. "A catalog of small proteins from the global microbiome," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
- Mirjana Domazet-Lošo & Tin Široki & Korina Šimičević & Tomislav Domazet-Lošo, 2024. "Macroevolutionary dynamics of gene family gain and loss along multicellular eukaryotic lineages," Nature Communications, Nature, vol. 15(1), pages 1-22, December.
- Patrick Bryant & Frank Noé, 2024. "Structure prediction of alternative protein conformations," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
- David Moi & Shunsuke Nishio & Xiaohui Li & Clari Valansi & Mauricio Langleib & Nicolas G. Brukman & Kateryna Flyak & Christophe Dessimoz & Daniele de Sanctis & Kathryn Tunyasuvunakool & John Jumper & , 2022. "Discovery of archaeal fusexins homologous to eukaryotic HAP2/GCS1 gamete fusion proteins," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
- Shuqi Qin & Dianye Zhang & Bin Wei & Yuanhe Yang, 2024. "Dual roles of microbes in mediating soil carbon dynamics in response to warming," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
- Jessie Lynda Fields & Hua Zhang & Nathan F. Bellis & Holly A. Petersen & Sajal K. Halder & Shane T. Rich-New & Mart Krupovic & Hui Wu & Fengbin Wang, 2024. "Structural diversity and clustering of bacterial flagellar outer domains," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
- Daniel P. Cetnar & Ayaan Hossain & Grace E. Vezeau & Howard M. Salis, 2024. "Predicting synthetic mRNA stability using massively parallel kinetic measurements, biophysical modeling, and machine learning," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
- Jeffrey A. Ruffolo & Lee-Shin Chu & Sai Pooja Mahajan & Jeffrey J. Gray, 2023. "Fast, accurate antibody structure prediction from deep learning on massive set of natural antibodies," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
- Ivan Koludarov & Tobias Senoner & Timothy N. W. Jackson & Daniel Dashevsky & Michael Heinzinger & Steven D. Aird & Burkhard Rost, 2023. "Domain loss enabled evolution of novel functions in the snake three-finger toxin gene superfamily," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
- Bin Ma & Caiyu Lu & Yiling Wang & Jingwen Yu & Kankan Zhao & Ran Xue & Hao Ren & Xiaofei Lv & Ronghui Pan & Jiabao Zhang & Yongguan Zhu & Jianming Xu, 2023. "A genomic catalogue of soil microbiomes boosts mining of biodiversity and genetic resources," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
- Julia Koehler Leman & Pawel Szczerbiak & P. Douglas Renfrew & Vladimir Gligorijevic & Daniel Berenberg & Tommi Vatanen & Bryn C. Taylor & Chris Chandler & Stefan Janssen & Andras Pataki & Nick Carrier, 2023. "Sequence-structure-function relationships in the microbial protein universe," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
- Guillermo Guerrero-Egido & Adrian Pintado & Kevin M. Bretscher & Luisa-Maria Arias-Giraldo & Joseph N. Paulson & Herman P. Spaink & Dennis Claessen & Cayo Ramos & Francisco M. Cazorla & Marnix H. Mede, 2024. "bacLIFE: a user-friendly computational workflow for genome analysis and prediction of lifestyle-associated genes in bacteria," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
- Casey N. Grun & Ruchi Jain & Maren Schniederberend & Charles B. Shoemaker & Bryce Nelson & Barbara I. Kazmierczak, 2024. "Bacterial cell surface characterization by phage display coupled to high-throughput sequencing," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
Corrections
All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-47371-9. See general information about how to correct material in RePEc.
If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.
If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .
If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.
For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .
Please note that corrections may take a couple of weeks to filter through the various RePEc services.