Paper Info
Title
Automated genome sequence analysis and annotation
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 overinterpretation of results are discussed with proposals for improvement. A conservative definition for reporting 'new findings' thar rakes account of database maturity is presented along with examples of possible kinds of discover ies (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 nn integrated automatic approach using multiple databases and search methods applied in art objective and repeatable manner.
Year
DOI
Venue
1999
10.1093/bioinformatics/15.5.391
BIOINFORMATICS
Field
DocType
Volume
Data mining,Multiple-criteria decision analysis,Sequence database,Annotation,Genome project,Computer science,Database search engine,Biological database,Bioinformatics,Sequence analysis,Web server
Journal
15
Issue
ISSN
Citations 
5
1367-4803
60
PageRank 
References 
Authors
10.59
17
11
Name
Order
Citations
PageRank
Miguel A. Andrade1657116.78
N. P. Brown26010.59
Christophe Leroy316932.50
S. Hörsch49117.76
Antoine De Daruvar513625.56
C. Reich66010.59
A. Franchini76010.59
Javier Tamames816524.27
Alfonso Valencia92577322.43
Christos A. Ouzounis10879200.77
Chris Sander11469157.99