The past, present and future of genome-wide re-annotation.

Genome biology ·Vol. 3 ·No. 2 ·2002-00-00 ·Pages COMMENT2001

Ouzounis CA, Karp PD

Abstract

Annotation, the process by which structural or functional information is inferred for genes or proteins, is crucial for obtaining value from genome sequences. We define the process of annotating a previously annotated genome sequence as 're-annotation', and examine the strengths and weaknesses of current manual and automatic genome-wide re-annotation approaches.

MeSH Terms

Computational Biology/standards,trends Databases, Genetic/standards,trends Databases, Protein/standards,trends Genome Quality Control

Authors & Affiliations

2 authors, click to expand affiliations / ORCID

Ouzounis Christos A

Bioinformatics Research Group, AI Center, SRI International, Menlo Park, CA 94025, USA. pkarp@ai.sri.com

Karp Peter D

References (37)

37 references, click to expand

More Haemophilus and Mycoplasma genes.
Science. 1996 Mar 1;271(5253):1302-3; author reply 1303-4 PMID: 8638118
New protein functions in yeast chromosome VIII.
Protein Sci. 1995 Nov;4(11):2424-8 PMID: 8563640
Metabolism and evolution of Haemophilus influenzae deduced from a whole-genome comparison with Escherichia coli.
Curr Biol. 1996 Mar 1;6(3):279-91 PMID: 8805245
HinCyc: a knowledge base of the complete genome and metabolic pathways of H. influenzae.
Proc Int Conf Intell Syst Mol Biol. 1996;4:116-24 PMID: 8877511
Sequence analysis of the Methanococcus jannaschii genome and the prediction of protein function.
Comput Appl Biosci. 1997 Aug;13(4):481-3 PMID: 9283767
Prediction of enzyme classification from protein sequence without the use of sequence similarity.
Proc Int Conf Intell Syst Mol Biol. 1997;5:92-9 PMID: 9322021
Predicting enzyme function from sequence: a systematic appraisal.
Proc Int Conf Intell Syst Mol Biol. 1997;5:276-83 PMID: 9322050
The challenges of genome sequence annotation or "the devil is in the details".
Nat Biotechnol. 1997 Nov;15(12):1222-3 PMID: 9359093
Comparison of archaeal and bacterial genomes: computer analysis of protein sequences predicts novel functions and suggests a chimeric origin for the archaea.
Mol Microbiol. 1997 Aug;25(4):619-37 PMID: 9379893
Characterization of new proteins found by analysis of short open reading frames from the full yeast genome.
Yeast. 1997 Nov;13(14):1363-74 PMID: 9392081
Reconstruction of amino acid biosynthesis pathways from the complete genome sequence.
Genome Res. 1998 Mar;8(3):203-10 PMID: 9521924
Methanococcus jannaschii genome: revisited.
Microb Comp Genomics. 1996;1(4):329-38 PMID: 9689216
Errors in genome reviews.
Science. 1998 Sep 4;281(5382):1457 PMID: 9750114
Errors in genome annotation.
Trends Genet. 1999 Apr;15(4):132-3 PMID: 10203816
Whole-genome sequence annotation: 'Going wrong with confidence'.
Mol Microbiol. 1999 May;32(4):886-7 PMID: 10361291
Automated genome sequence analysis and annotation.
Bioinformatics. 1999 May;15(5):391-412 PMID: 10366660
Reproducibility in genome sequence annotation: the Plasmodium falciparum chromosome 2 case.
FEBS Lett. 1999 May 28;451(3):354-5 PMID: 10371220
Some measures of comparative performance in the three CASPs.
Proteins. 1999;Suppl 3:231-7 PMID: 10526374
Novel coding regions in four complete archaeal genomes.
Nucleic Acids Res. 1999 Nov 15;27(22):4405-8 PMID: 10536149
'Going wrong with confidence': misleading sequence analyses of CiaB and clpX.
Mol Microbiol. 1999 Oct;34(1):195 PMID: 10540297
Assessing annotation transfer for genomics: quantifying the relations between protein sequence, structure and function through traditional and probabilistic scores.
J Mol Biol. 2000 Mar 17;297(1):233-49 PMID: 10704319
Annotating eukaryote genomes.
Curr Opin Struct Biol. 2000 Jun;10(3):349-54 PMID: 10851187
Debates over credit for the annotation of genomes.
Nature. 2000 Jun 15;405(6788):719 PMID: 10866159
Re-annotating the Mycoplasma pneumoniae genome sequence: adding value, function and reading frames.
Nucleic Acids Res. 2000 Sep 1;28(17):3278-88 PMID: 10954595
Predicting protein function by genomic context: quantitative evaluation and qualitative inferences.
Genome Res. 2000 Aug;10(8):1204-10 PMID: 10958638
Recent developments and future directions in computational genomics.
FEBS Lett. 2000 Aug 25;480(1):42-8 PMID: 10967327
Analysis of the Thermotoga maritima genome combining a variety of sequence similarity and genome context tools.
Nucleic Acids Res. 2000 Nov 15;28(22):4573-6 PMID: 11071948
Genome sequences and great expectations.
Genome Biol. 2001;2(1):INTERACTIONS0001 PMID: 11178275
Towards understanding the first genome sequence of a crenarchaeon by genome annotation using clusters of orthologous groups of proteins (COGs).
Genome Biol. 2000;1(5):RESEARCH0009 PMID: 11178258
Functional and structural genomics using PEDANT.
Bioinformatics. 2001 Jan;17(1):44-57 PMID: 11222261
Intrinsic errors in genome annotation.
Trends Genet. 2001 Aug;17(8):429-31 PMID: 11485799
What's in a genome?
Nature. 1992 Jul 23;358(6384):287 PMID: 1641000
Comprehensive sequence analysis of the 182 predicted open reading frames of yeast chromosome III.
Protein Sci. 1992 Dec;1(12):1677-90 PMID: 1304897
Yeast chromosome III: new gene functions.
EMBO J. 1994 Feb 1;13(3):493-503 PMID: 8313894
Novel protein families in archaean genomes.
Nucleic Acids Res. 1995 Feb 25;23(4):565-70 PMID: 7899076
Challenging times for bioinformatics.
Nature. 1995 Aug 24;376(6542):647-8 PMID: 7651513
Novelties from the complete genome of Mycoplasma genitalium.
Mol Microbiol. 1996 May;20(4):898-900 PMID: 8793887

Article Info

Journal

Genome biology

Abbr.

Genome Biol

ISSN

1474-760X

DOI

10.1186/gb-2002-3-2-comment2001

pkarp@ai.sri.com

Published

2002-00-00

Epub

2002-00-31

Pages

COMMENT2001

Language

English

Region

England

NLM ID

100960660

PMCID

PMC139008

Subset

External Links

PubMed source DOI: 10.1186/gb-2002-3-2-comment2001 PMC Full Text View journal details

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