ProtoNet 6.0: Organizing 10 Million Protein Sequences in a Compact Hierarchical Family Tree

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2011 Nov 29

PMID 22121228

Citations 23

Authors

Nadav Rappoport

Solange Karsenty

Amos Stern

Nathan Linial

Michal Linial

Affiliations

Soon will be listed here.

Abstract

ProtoNet 6.0 (http://www.protonet.cs.huji.ac.il) is a data structure of protein families that cover the protein sequence space. These families are generated through an unsupervised bottom-up clustering algorithm. This algorithm organizes large sets of proteins in a hierarchical tree that yields high-quality protein families. The 2012 ProtoNet (Version 6.0) tree includes over 9 million proteins of which 5.5% come from UniProtKB/SwissProt and the rest from UniProtKB/TrEMBL. The hierarchical tree structure is based on an all-against-all comparison of 2.5 million representatives of UniRef50. Rigorous annotation-based quality tests prune the tree to most informative 162,088 clusters. Every high-quality cluster is assigned a ProtoName that reflects the most significant annotations of its proteins. These annotations are dominated by GO terms, UniProt/Swiss-Prot keywords and InterPro. ProtoNet 6.0 operates in a default mode. When used in the advanced mode, this data structure offers the user a view of the family tree at any desired level of resolution. Systematic comparisons with previous versions of ProtoNet are carried out. They show how our view of protein families evolves, as larger parts of the sequence space become known. ProtoNet 6.0 provides numerous tools to navigate the hierarchy of clusters.

Citing Articles

Identification of resistance gene analogs of the NBS-LRR family through transcriptome probing and prediction of the expressome of under dieback disease stress.

Ijaz S, Ul Haq I, Ahmad Khan I, Ali H, Kaur S, Razzaq H Front Genet. 2022; 13:1036029.

PMID: 36276980 PMC: 9585183. DOI: 10.3389/fgene.2022.1036029.

In silico Functional Annotation and Characterization of Hypothetical Proteins from FGI94.

Prabhu D, Rajamanikandan S, Anusha S, Chowdary M, Veerapandiyan M, Jeyakanthan J Biol Bull Russ Acad Sci. 2020; 47(4):319-331.

PMID: 32834707 PMC: 7394047. DOI: 10.1134/S1062359020300019.

Functional and Structural Analysis of Predicted Proteins Obtained from Minisatellite 33.15-Tagged Transcript pAKT-45 Variants.

Shahbaaz M, Al-Samghan A, Malik A, Afaq S, Alwabli A, Ahmad I Biomed Res Int. 2020; 2020:2562950.

PMID: 32566673 PMC: 7273396. DOI: 10.1155/2020/2562950.

Functional Prediction of Hypothetical Proteins from Shigella flexneri and Validation of the Predicted Models by Using ROC Curve Analysis.

Gazi M, Mahmud S, Fahim S, Kibria M, Palit P, Islam M Genomics Inform. 2019; 16(4):e26.

PMID: 30602087 PMC: 6440662. DOI: 10.5808/GI.2018.16.4.e26.

A Computational Approach Using Bioinformatics to Screening Drug Targets for Species.

Chavez-Fumagalli M, Schneider M, Pagliara Lage D, de Sousa Vieira Tavares G, Mendonca D, Santos T Evid Based Complement Alternat Med. 2018; 2018:6813467.

PMID: 29785196 PMC: 5896251. DOI: 10.1155/2018/6813467.

References

Portugaly E, Linial N, Linial M . EVEREST: a collection of evolutionary conserved protein domains. Nucleic Acids Res. 2006; 35(Database issue):D241-6. PMC: 1669739. DOI: 10.1093/nar/gkl850. View

Sasson O, Kaplan N, Linial M . Functional annotation prediction: all for one and one for all. Protein Sci. 2006; 15(6):1557-62. PMC: 2242553. DOI: 10.1110/ps.062185706. View

Suzek B, Huang H, McGarvey P, Mazumder R, Wu C . UniRef: comprehensive and non-redundant UniProt reference clusters. Bioinformatics. 2007; 23(10):1282-8. DOI: 10.1093/bioinformatics/btm098. View

Wu C, Nikolskaya A, Huang H, Yeh L, Natale D, Vinayaka C . PIRSF: family classification system at the Protein Information Resource. Nucleic Acids Res. 2003; 32(Database issue):D112-4. PMC: 308831. DOI: 10.1093/nar/gkh097. View

Attwood T, Bradley P, Flower D, Gaulton A, Maudling N, Mitchell A . PRINTS and its automatic supplement, prePRINTS. Nucleic Acids Res. 2003; 31(1):400-2. PMC: 165477. DOI: 10.1093/nar/gkg030. View

Pazos F, Sternberg M . Automated prediction of protein function and detection of functional sites from structure. Proc Natl Acad Sci U S A. 2004; 101(41):14754-9. PMC: 522026. DOI: 10.1073/pnas.0404569101. View

Bairoch A . The ENZYME database in 2000. Nucleic Acids Res. 1999; 28(1):304-5. PMC: 102465. DOI: 10.1093/nar/28.1.304. View

Petryszak R, Kretschmann E, Wieser D, Apweiler R . The predictive power of the CluSTr database. Bioinformatics. 2005; 21(18):3604-9. DOI: 10.1093/bioinformatics/bti542. View

Letunic I, Doerks T, Bork P . SMART 6: recent updates and new developments. Nucleic Acids Res. 2008; 37(Database issue):D229-32. PMC: 2686533. DOI: 10.1093/nar/gkn808. View

10.

Loewenstein Y, Portugaly E, Fromer M, Linial M . Efficient algorithms for accurate hierarchical clustering of huge datasets: tackling the entire protein space. Bioinformatics. 2008; 24(13):i41-9. PMC: 2718652. DOI: 10.1093/bioinformatics/btn174. View

11.

Barrell D, Dimmer E, Huntley R, Binns D, ODonovan C, Apweiler R . The GOA database in 2009--an integrated Gene Ontology Annotation resource. Nucleic Acids Res. 2008; 37(Database issue):D396-403. PMC: 2686469. DOI: 10.1093/nar/gkn803. View

12.

Watson J, Sanderson S, Ezersky A, Savchenko A, Edwards A, Orengo C . Towards fully automated structure-based function prediction in structural genomics: a case study. J Mol Biol. 2007; 367(5):1511-22. PMC: 2566530. DOI: 10.1016/j.jmb.2007.01.063. View

13.

Henikoff J, GREENE E, Pietrokovski S, Henikoff S . Increased coverage of protein families with the blocks database servers. Nucleic Acids Res. 1999; 28(1):228-30. PMC: 102407. DOI: 10.1093/nar/28.1.228. View

14.

Bru C, Courcelle E, Carrere S, Beausse Y, Dalmar S, Kahn D . The ProDom database of protein domain families: more emphasis on 3D. Nucleic Acids Res. 2004; 33(Database issue):D212-5. PMC: 539988. DOI: 10.1093/nar/gki034. View

15.

Rappoport N, Fromer M, Schweiger R, Linial M . PANDORA: analysis of protein and peptide sets through the hierarchical integration of annotations. Nucleic Acids Res. 2010; 38(Web Server issue):W84-9. PMC: 2896089. DOI: 10.1093/nar/gkq320. View

16.

Finn R, Mistry J, Tate J, Coggill P, Heger A, Pollington J . The Pfam protein families database. Nucleic Acids Res. 2009; 38(Database issue):D211-22. PMC: 2808889. DOI: 10.1093/nar/gkp985. View

17.

Yooseph S, Sutton G, Rusch D, Halpern A, Williamson S, Remington K . The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PLoS Biol. 2007; 5(3):e16. PMC: 1821046. DOI: 10.1371/journal.pbio.0050016. View

18.

Marchler-Bauer A, Lu S, Anderson J, Chitsaz F, Derbyshire M, DeWeese-Scott C . CDD: a Conserved Domain Database for the functional annotation of proteins. Nucleic Acids Res. 2010; 39(Database issue):D225-9. PMC: 3013737. DOI: 10.1093/nar/gkq1189. View

19.

Hunter S, Apweiler R, Attwood T, Bairoch A, Bateman A, Binns D . InterPro: the integrative protein signature database. Nucleic Acids Res. 2008; 37(Database issue):D211-5. PMC: 2686546. DOI: 10.1093/nar/gkn785. View

20.

Mi H, Dong Q, Muruganujan A, Gaudet P, Lewis S, Thomas P . PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium. Nucleic Acids Res. 2009; 38(Database issue):D204-10. PMC: 2808919. DOI: 10.1093/nar/gkp1019. View