by Paolo Fontana, Alessandro Cestaro, Riccardo Velasco, Elide Formentin, Stefano Toppo
Abstract:
Background: Large-scale sequencing projects have now become routine lab practice and this has led to the development of a new generation of tools involving function prediction methods, bringing the latter back to the fore. The advent of Gene Ontology, with its structured vocabulary and paradigm, has provided computational biologists with an appropriate means for this task. Methodology: We present here a novel method called ARGOT (Annotation Retrieval of Gene Ontology Terms) that is able to process quickly thousands of sequences for functional inference. The tool exploits for the first time an integrated approach which combines clustering of GO terms, based on their semantic similarities, with a weighting scheme which assesses retrieved hits sharing a certain number of biological features with the sequence to be annotated. These hits may be obtained by different methods and in this work we have based ARGOT processing on BLAST results. Conclusions: The extensive benchmark involved 10,000 protein sequences, the complete S. cerevisiae genome and a small subset of proteins for purposes of comparison with other available tools. The algorithm was proven to outperform existing methods and to be suitable for function prediction of single proteins due to its high degree of sensitivity, specificity and coverage.
Reference:
Rapid Annotation of Anonymous Sequences from Genome Projects Using Semantic Similarities and a Weighting Scheme in Gene Ontology (Paolo Fontana, Alessandro Cestaro, Riccardo Velasco, Elide Formentin, Stefano Toppo), In PLoS ONE (Sridhar Hannenhalli, ed.), Public Library of Science, volume 4, 2009.
Bibtex Entry:
@article{Fontana2009a,
abstract = {Background: Large-scale sequencing projects have now become routine lab practice and this has led to the development of a new generation of tools involving function prediction methods, bringing the latter back to the fore. The advent of Gene Ontology, with its structured vocabulary and paradigm, has provided computational biologists with an appropriate means for this task. Methodology: We present here a novel method called ARGOT (Annotation Retrieval of Gene Ontology Terms) that is able to process quickly thousands of sequences for functional inference. The tool exploits for the first time an integrated approach which combines clustering of GO terms, based on their semantic similarities, with a weighting scheme which assesses retrieved hits sharing a certain number of biological features with the sequence to be annotated. These hits may be obtained by different methods and in this work we have based ARGOT processing on BLAST results. Conclusions: The extensive benchmark involved 10,000 protein sequences, the complete S. cerevisiae genome and a small subset of proteins for purposes of comparison with other available tools. The algorithm was proven to outperform existing methods and to be suitable for function prediction of single proteins due to its high degree of sensitivity, specificity and coverage.},
annote = {
From Duplicate 2 (
Rapid Annotation of Anonymous Sequences from Genome Projects Using Semantic Similarities and a Weighting Scheme in Gene Ontology
- Fontana, Paolo; Cestaro, Alessandro; Velasco, Riccardo; Formentin, Elide; Toppo, Stefano )
},
author = {Fontana, Paolo and Cestaro, Alessandro and Velasco, Riccardo and Formentin, Elide and Toppo, Stefano},
editor = {Hannenhalli, Sridhar},
institution = {FEM-IASMA Research Center, San Michele all'Adige (TN), Italy.},
journal = {PLoS ONE},
keywords = {SML-LIB-BIBLIO,Semantic Similarity,lang:ENG,semantic similarity},
mendeley-tags = {SML-LIB-BIBLIO,lang:ENG,semantic similarity},
number = {2},
pages = {15},
publisher = {Public Library of Science},
title = {{Rapid Annotation of Anonymous Sequences from Genome Projects Using Semantic Similarities and a Weighting Scheme in Gene Ontology}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2645684\&tool=pmcentrez\&rendertype=abstract},
volume = {4},
year = {2009}
}