ArticleNucleic acids research2012
ProtoNet 6.0: organizing 10 million protein sequences in a compact hierarchical family tree.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Identification of resistance gene analogs of the NBS-LRR family through transcriptome probing andFrontiers in genetics · 2022Article
- In silico Functional Annotation and Characterization of Hypothetical Proteins fromBiology bulletin of the Russian Academy of Sciences · 2020Article
- Functional and Structural Analysis of Predicted Proteins Obtained fromBioMed research international · 2020Article
- Functional Prediction of Hypothetical Proteins from Shigella flexneri and Validation of the Predicted Models by Using ROC Curve Analysis.Genomics & informatics · 2018Article
- Small Myristoylated Protein-3, Identified as a Potential Virulence Factor in Leishmania amazonensis, Proves to be a Protective Antigen against Visceral Leishmaniasis.International journal of molecular sciences · 2018Article
- A Computational Approach Using Bioinformatics to Screening Drug Targets forEvidence-based complementary and alternative medicine : eCAM · 2018Article
- Article
- Protein Bioinformatics Databases and Resources.Methods in molecular biology (Clifton, N.J.) · 2017Review
- Percolation in protein sequence space.PloS one · 2017Article
- Sequence Analysis of Hypothetical Proteins fromGenomics & informatics · 2016Article
- Structure-based function analysis of putative conserved proteins with isomerase activity from Haemophilus influenzae.3 Biotech · 2015Article
- Structure-based functional annotation of putative conserved proteins having lyase activity from Haemophilus influenzae.3 Biotech · 2015Article
- Identification of a Novel Mucin Gene HCG22 Associated With Steroid-Induced Ocular Hypertension.Investigative ophthalmology & visual science · 2015Article
- ProtoBug: functional families from the complete proteomes of insects.Database : the journal of biological databases and curation · 2015Article
- Entropy-driven partitioning of the hierarchical protein space.Bioinformatics (Oxford, England) · 2014Article
- SIMAP--the database of all-against-all protein sequence similarities and annotations with new interfaces and increased coverage.Nucleic acids research · 2014Article
- Integrating in silico resources to map a signaling network.Methods in molecular biology (Clifton, N.J.) · 2014Article
- kClust: fast and sensitive clustering of large protein sequence databases.BMC bioinformatics · 2013Article
- ProtoNet: charting the expanding universe of protein sequences.Nature biotechnology · 2013Article
- Functional inference by ProtoNet family tree: the uncharacterized proteome of Daphnia pulex.BMC bioinformatics · 2013Article
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5 authors.
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No grant is acknowledged in the PubMed record.
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.
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