title: Rapid annotation of anonymous sequences from genome projects using semantic similarities and a weighting scheme in gene ontology.
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.
  
  
  METHODS
  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.
authors.affiliation: FEM-IASMA Research Center, San Michele all'Adige (TN), Italy.
authors.forename: Paolo
authors.initials: P
authors.lastname: Fontana
authors.forename: Alessandro
authors.initials: A
authors.lastname: Cestaro
authors.forename: Riccardo
authors.initials: R
authors.lastname: Velasco
authors.forename: Elide
authors.initials: E
authors.lastname: Formentin
authors.forename: Stefano
authors.initials: S
authors.lastname: Toppo
mesh_terms: D000465:Algorithms; D030541:Databases, Genetic; D005656:Fungal Proteins / Q000235:genetics; D016681:Genome, Fungal; D016247:Information Storage and Retrieval; D012441:Saccharomyces cerevisiae / Q000235:genetics
chemical_list: D005656:Fungal Proteins