FFPred 3: feature-based function prediction for all Gene Ontology domains
By Domenico Cozzetto, Federico Minneci, Hannah Currant, David T. Jones. 2016
118 citations recorded by the source corpus.
Predicting protein function has been a major goal of bioinformatics for several decades, and it has gained fresh momentum thanks to recent community-wide blind tests aimed at benchmarking available tools on a genomic scale. Sequence-based predictors, especially those performing homology-based transfers, remain the most popular but increasing understanding of their limitations has stimulated the development of complementary approaches, which mostly exploit machine learning. Here we present FFPred 3, which is intended for assigning Gene Ontology terms to human protein chains, when homology with characterized proteins can provide little aid. Predictions are made by scanning the input sequences against an array of Support Vector Machines (SVMs), each examining the relationship between protein function and biophysical attributes describing secondary structure, transmembrane helices, intrinsically disordered regions, signal peptides and other motifs. This update features a larger SVM library that extends its coverage to the cellular component sub-ontology for the first time, prompted by the establishment of a dedicated evaluation category within the Critical Assessment of Functional Annotation. The effectiveness of this approach is demonstrated through benchmarking experiments, and its usefulness is illustrated by analysing the potential functional consequences of alternative splicing in human and their relationship to patterns of biological features.
Subfields: Molecular Biology
How researchers see this paper
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In Molecular Biology
- David T. Jones
- Daniel W. A. Buchan
- Nadav Brandes
- Dan Ofer
- Michal Linial
- Markus A. Wenzel
- Nils Strodthoff
- Wojciech Samek
Citations in the corpus
- UDSMProt: universal deep sequence models for protein classification (2019, methodology): “State-of-the-art: Similar to enzyme class prediction, the first proposed approaches in this field relied on handcrafted features like functionally discriminating residues (FDR) with PSSM [4] and classification models consisting of an array of Support Vector Machines [5].”
- The language of proteins: NLP, machine learning & protein sequences (2021, background): “Other global properties include thermal stability, source organism, and functional protein annotations (e.g. gene ontology, GO) such as antiviral activity [79,64,41,84,5,25].”
- The PSIPRED Protein Analysis Workbench: 20 years on (2019, methodology): “Many of the predictors offered by our service, such as PSIPRED or FFPred (17), begin with a comprehensive protein database search using PSIBLAST (30).”