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Automated genome sequence analysis and annotation

Item Type:Article
Title:Automated genome sequence analysis and annotation
Creators Name:Andrade, M.A. and Brown, N.P. and Leroy, C. and Hoersch, S. and de Daruvar, A. and Reich, C. and Franchini, A. and Tamames, J. and Valencia, A. and Ouzounis, C. and Sander, C.
Abstract:MOTIVATION: Large-scale genome projects generate a rapidly increasing number of sequences, most of them biochemically uncharacterized. Research in bioinformatics contributes to the development of methods for the computational characterization of these sequences. However, the installation and application of these methods require experience and are time consuming. RESULTS: We present here an automatic system for preliminary functional annotation of protein sequences that has been applied to the analysis of sets of sequences from complete genomes, both to refine overall performance and to make new discoveries comparable to those made by human experts. The GeneQuiz system includes a Web-based browser that allows examination of the evidence leading to an automatic annotation and offers additional information, views of the results, and links to biological databases that complement the automatic analysis. System structure and operating principles concerning the use of multiple sequence databases, underlying sequence analysis tools, lexical analyses of database annotations and decision criteria for functional assignments are detailed. The system makes automatic quality assessments of results based on prior experience with the underlying sequence analysis tools; overall error rates in functional assignment are estimated at 2.5-5% for cases annotated with highest reliability ('clear' cases). Sources of over-interpretation of results are discussed with proposals for improvement. A conservative definition for reporting 'new findings' that takes account of database maturity is presented along with examples of possible kinds of discoveries (new function, family and superfamily) made by the system. System performance in relation to sequence database coverage, database dynamics and database search methods is analysed, demonstrating the inherent advantages of an integrated automatic approach using multiple databases and search methods applied in an objective and repeatable manner. AVAILABILITY: The GeneQuiz system is publicly available for analysis of protein sequences through a Web server at http://www.sander.ebi.ac. uk/gqsrv/submit
Keywords:Amino Acid Sequence, Automation, Computer Systems, Factual Databases, Molecular Sequence Data, Proteins, Sequence Analysis, Software
Publisher:Oxford University Press
Page Range:391-412
Date:May 1999
Official Publication:http://bioinformatics.oxfordjournals.org/cgi/content/abstract/15/5/391
PubMed:View item in PubMed

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