Automated genome sequence analysis and annotation

Publication type:
Journal article
Metadata:
Autoren
  • MA Andrade
  • NP Brown
  • C Leroy
  • S Hoersch
  • A de Daruvar
  • C Reich
  • A Franchini
  • J Tamames
  • A Valencia
  • C Ouzounis
  • C Sander
Autoren-URL
https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=fis-test-1&SrcAuth=WosAPI&KeyUT=WOS:000081230200008&DestLinkType=FullRecord&DestApp=WOS_CPL
DOI
10.1093/bioinformatics/15.5.391
eISSN
1460-2059
Externe Identifier
  • Clarivate Analytics Document Solution ID: 212RN
  • PubMed Identifier: 10366660
ISSN
1367-4803
Ausgabe der Veröffentlichung
5
Zeitschrift
BIOINFORMATICS
Paginierung
391 - 412
Datum der Veröffentlichung
1999
Status
Published
Titel
Automated genome sequence analysis and annotation
Sub types
  • Article
Ausgabe der Zeitschrift
15

Data source: Web of Science (Lite)

Other metadata sources:
Abstract
<jats:title>Abstract</jats:title> <jats:p>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</jats:p>
Autoren
  • MA Andrade
  • NP Brown
  • C Leroy
  • S Hoersch
  • A de Daruvar
  • C Reich
  • A Franchini
  • J Tamames
  • A Valencia
  • C Ouzounis
  • C Sander
DOI
10.1093/bioinformatics/15.5.391
eISSN
1367-4811
ISSN
1367-4803
Ausgabe der Veröffentlichung
5
Zeitschrift
Bioinformatics
Sprache
en
Online publication date
1999
Paginierung
391 - 412
Datum der Veröffentlichung
1999
Status
Published
Herausgeber
Oxford University Press (OUP)
Herausgeber URL
http://dx.doi.org/10.1093/bioinformatics/15.5.391
Datum der Datenerfassung
2023
Titel
Automated genome sequence analysis and annotation.
Ausgabe der Zeitschrift
15

Data source: Crossref

Abstract
<h4>Motivation</h4>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.<h4>Results</h4>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.<h4>Availability</h4>The GeneQuiz system is publicly available for analysis of protein sequences through a Web server at http://www.sander.ebi.ac. uk/gqsrv/submit
Addresses
  • European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK.
Autoren
  • MA Andrade
  • NP Brown
  • C Leroy
  • S Hoersch
  • A de Daruvar
  • C Reich
  • A Franchini
  • J Tamames
  • A Valencia
  • C Ouzounis
  • C Sander
DOI
10.1093/bioinformatics/15.5.391
eISSN
1367-4811
Externe Identifier
  • PubMed Identifier: 10366660
Open access
false
ISSN
1367-4803
Ausgabe der Veröffentlichung
5
Zeitschrift
Bioinformatics (Oxford, England)
Schlüsselwörter
  • Humans
  • Proteins
  • Sequence Analysis
  • Amino Acid Sequence
  • Automation
  • Computer Systems
  • Software
  • Molecular Sequence Data
  • Databases, Factual
Sprache
eng
Medium
Print
Paginierung
391 - 412
Datum der Veröffentlichung
1999
Status
Published
Datum der Datenerfassung
1999
Titel
Automated genome sequence analysis and annotation.
Sub types
  • Journal Article
Ausgabe der Zeitschrift
15

Data source: Europe PubMed Central

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
Autoren
  • MA Andrade
  • NP Brown
  • C Leroy
  • S Hoersch
  • A de Daruvar
  • C Reich
  • A Franchini
  • J Tamames
  • A Valencia
  • C Ouzounis
  • C Sander
Autoren-URL
https://www.ncbi.nlm.nih.gov/pubmed/10366660
DOI
10.1093/bioinformatics/15.5.391
ISSN
1367-4803
Ausgabe der Veröffentlichung
5
Zeitschrift
Bioinformatics
Schlüsselwörter
  • Amino Acid Sequence
  • Automation
  • Computer Systems
  • Databases, Factual
  • Humans
  • Molecular Sequence Data
  • Proteins
  • Sequence Analysis
  • Software
Sprache
eng
Country
England
Paginierung
391 - 412
PII
btc053
Datum der Veröffentlichung
1999
Status
Published
Datum, an dem der Datensatz öffentlich gemacht wurde
1999
Titel
Automated genome sequence analysis and annotation.
Sub types
  • Journal Article
Ausgabe der Zeitschrift
15

Data source: PubMed

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