ArticleNucleic acids research2015
SIFTER search: a web server for accurate phylogeny-based protein function prediction.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Article
- A Survey of Biological Function Prediction Methods with Focus on Natural Language Processing (NLP) and Large Language Models (LLM).Methods in molecular biology (Clifton, N.J.) · 2025Article
- Cross-Species Insights into PR Proteins: A Comprehensive Study ofIndian journal of microbiology · 2024Article
- Clustering protein functional families at large scale with hierarchical approaches.Protein science : a publication of the Protein Society · 2024Article
- Domain-PFP allows protein function prediction using function-aware domain embedding representations.Communications biology · 2023Article
- Domain-PFP: Protein Function Prediction Using Function-Aware Domain Embedding Representations.bioRxiv : the preprint server for biology · 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
- Investigation of Antidepressant Properties of Yohimbine by Employing Structure-Based Computational Assessments.Current issues in molecular biology · 2021Article
- DeepGOWeb: fast and accurate protein function prediction on the (Semantic) Web.Nucleic acids research · 2021Article
- Protein functional annotation of simultaneously improved stability, accuracy and false discovery rate achieved by a sequence-based deep learning.Briefings in bioinformatics · 2020Article
- Residue Cluster Classes: A Unified Protein Representation for Efficient Structural and Functional Classification.Entropy (Basel, Switzerland) · 2020Article
- PvP01-DB: computational structural and functional characterization of soluble proteome of PvP01 strain of Plasmodium vivax.Database : the journal of biological databases and curation · 2020Article
- Functional Prediction and Assignment ofFrontiers in genetics · 2020Article
- UNIPred-Web: a web tool for the integration and visualization of biomolecular networks for protein function prediction.BMC bioinformatics · 2019Article
- NetGO: improving large-scale protein function prediction with massive network information.Nucleic acids research · 2019Article
- INGA 2.0: improving protein function prediction for the dark proteome.Nucleic acids research · 2019Article
- Phylo-PFP: improved automated protein function prediction using phylogenetic distance of distantly related sequences.Bioinformatics (Oxford, England) · 2019Article
- Effusion: prediction of protein function from sequence similarity networks.Bioinformatics (Oxford, England) · 2019Article
- Assessing the Performances of Protein Function Prediction Algorithms from the Perspectives of Identification Accuracy and False Discovery Rate.International journal of molecular sciences · 2018Article
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3 authors.
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Abstract
We are awash in proteins discovered through high-throughput sequencing projects. As only a minuscule fraction of these have been experimentally characterized, computational methods are widely used for automated annotation. Here, we introduce a user-friendly web interface for accurate protein function prediction using the SIFTER algorithm. SIFTER is a state-of-the-art sequence-based gene molecular function prediction algorithm that uses a statistical model of function evolution to incorporate annotations throughout the phylogenetic tree. Due to the resources needed by the SIFTER algorithm, running SIFTER locally is not trivial for most users, especially for large-scale problems. The SIFTER web server thus provides access to precomputed predictions on 16 863 537 proteins from 232 403 species. Users can explore SIFTER predictions with queries for proteins, species, functions, and homologs of sequences not in the precomputed prediction set. The SIFTER web server is accessible at http://sifter.berkeley.edu/ and the source code can be downloaded.
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