ArticleGenome research2011
Genome-scale phylogenetic function annotation of large and diverse protein families.
Article in Genome research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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30 citing papers in PubMed, 62 citations in OpenAlex.
- Tuning the stator subunit of the flagellar motor with coiled-coil engineering.Protein science : a publication of the Protein Society · 2023Article
- Phylogenetic inference of the emergence of sequence modules and protein-protein interactions in the ADAMTS-TSL family.PLoS computational biology · 2023Article
- Multiple Profile Models Extract Features from Protein Sequence Data and Resolve Functional Diversity of Very Different Protein Families.Molecular biology and evolution · 2022Article
- Bayesian parameter estimation for automatic annotation of gene functions using observational data and phylogenetic trees.PLoS computational biology · 2021Article
- The ortholog conjecture revisited: the value of orthologs and paralogs in function prediction.Bioinformatics (Oxford, England) · 2020Article
- Effusion: prediction of protein function from sequence similarity networks.Bioinformatics (Oxford, England) · 2019Article
- Prioritising candidate genes causing QTL using hierarchical orthologous groups.Bioinformatics (Oxford, England) · 2018Article
- Identifying functional groups among the diverse, recombining antigenic var genes of the malaria parasite Plasmodium falciparum from a local community in Ghana.PLoS computational biology · 2018Article
- DeepGO: predicting protein functions from sequence and interactions using a deep ontology-aware classifier.Bioinformatics (Oxford, England) · 2018Article
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- Molecular Evolutionary Constraints that Determine the Avirulence State of Clostridium botulinum C2 Toxin.Journal of molecular evolution · 2017Article
- Computational and Experimental Studies of ADP-Ribosylation.Methods in molecular biology (Clifton, N.J.) · 2017Article
- PROSNET: INTEGRATING HOMOLOGY WITH MOLECULAR NETWORKS FOR PROTEIN FUNCTION PREDICTION.Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing · 2017Article
- Article
- Functional Annotations of Paralogs: A Blessing and a Curse.Life (Basel, Switzerland) · 2016Article
- INGA: protein function prediction combining interaction networks, domain assignments and sequence similarity.Nucleic acids research · 2015Article
- SIFTER search: a web server for accurate phylogeny-based protein function prediction.Nucleic acids research · 2015Article
- Exploring potential new floral organ morphogenesis genes of Arabidopsis thaliana using systems biology approach.Frontiers in plant science · 2015Article
- A Bayesian sampler for optimization of protein domain hierarchies.Journal of computational biology : a journal of computational molecular cell biology · 2014Article
- Functional clustering of immunoglobulin superfamily proteins with protein-protein interaction information calibrated hidden Markov model sequence profiles.Journal of molecular biology · 2014Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
The Statistical Inference of Function Through Evolutionary Relationships (SIFTER) framework uses a statistical graphical model that applies phylogenetic principles to automate precise protein function prediction. Here we present a revised approach (SIFTER version 2.0) that enables annotations on a genomic scale. SIFTER 2.0 produces equivalently precise predictions compared to the earlier version on a carefully studied family and on a collection of 100 protein families. We have added an approximation method to SIFTER 2.0 and show a 500-fold improvement in speed with minimal impact on prediction results in the functionally diverse sulfotransferase protein family. On the Nudix protein family, previously inaccessible to the SIFTER framework because of the 66 possible molecular functions, SIFTER achieved 47.4% accuracy on experimental data (where BLAST achieved 34.0%). Finally, we used SIFTER to annotate all of the Schizosaccharomyces pombe proteins with experimental functional characterizations, based on annotations from proteins in 46 fungal genomes. SIFTER precisely predicted molecular function for 45.5% of the characterized proteins in this genome, as compared with four current function prediction methods that precisely predicted function for 62.6%, 30.6%, 6.0%, and 5.7% of these proteins. We use both precision-recall curves and ROC analyses to compare these genome-scale predictions across the different methods and to assess performance on different types of applications. SIFTER 2.0 is capable of predicting protein molecular function for large and functionally diverse protein families using an approximate statistical model, enabling phylogenetics-based protein function prediction for genome-wide analyses. The code for SIFTER and protein family data are available at http://sifter.berkeley.edu.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.