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

Genome Biology

Volumn 3, Issue 2, 2002, Pages

  Ouzounis, Christos A ^a   Karp, Peter D ^b  

^a EUROPEAN BIOINFORMATICS INSTITUTE   (United Kingdom)

^b SRI INTERNATIONAL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; AUTOMATION; CONTROLLED STUDY; GENE FUNCTION; GENE STRUCTURE; GENOME ANALYSIS; INFORMATION PROCESSING; NONHUMAN; PROTEIN FUNCTION; PROTEIN STRUCTURE; SEQUENCE ANALYSIS;

COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; DATABASES, PROTEIN; GENOME; QUALITY CONTROL;

EID: 0036175276     PISSN: 14656906     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (40)

1. Novel protein families in archaean genomes
2. Debates over credit for the annotation of genomes
3. The challenges of genome sequence annotation or "the devil is in the details"
4. Automated genome sequence analysis and annotation
5. Genome sequences and great expectations
6. HinCyc: A knowledge base of the complete genome and metabolic pathways of H. influenzae
7. Metabolism and evolution of Haemophilus influenzae deduced from a whole-genome comparison with Escherichia coli
8. Challenging times for bioinformatics
9. More Haemophilus and Mycoplasma genes
10. Novelties from the complete genome of Mycoplasma genitalium
11. Predicting protein function by genomic context: Quantitative evaluation and qualitative inferences
12. Sequence analysis of the Methanococcus jannaschii genome and the prediction of protein function
13. Methanococcus jannaschi genome: Revisited
14. Whole-genome sequence annotation: 'Going wrong with confidence'
15. Comparison of archaeal and bacterial genomics: Computer analysis of protein sequences predicts novel functions and suggests a chimeric origin for the archaea
16. Novel coding regions in four complete archaeal genomes
17. Re-annotating the Mycoplasma pneumoniae genome sequence: Adding value, function and reading frames
18. Analysis of the Thermotoga maritima genome combining a variety of sequence similarity and genome context tools
19. What's in a genome?
20. Comprehensive sequence analysis of the 182 predicted open reading frames of yeast chromosome III
21. Yeast chromosome III: New gene functions
22. Characterization of new proteins found by analysis of short open reading frames from the full yeast genome
23. New protein functions in yeast chromosome VIII
24. Reproducibility in genome sequence annotation: The Plasmodium falciparum chromosome 2 case
25. Towards understanding the first genome sequence of a crenarchaeon by genome annotation using clusters of orthologous groups of proteins (COGs)
26. 'Going wrong with confidence': Misleading sequence analyses of CiaB and clpX
27. Prediction of Enzyme Classification from protein sequence without the use of sequence similarity
28. Predicting enzyme function from sequence: A systematic appraisal
29. Assessing annotation transfer for genomics: Quantifying the relations between protein sequence, structure and function through traditional and probabilistic scores
30. Reconstruction of amino acid biosynthesis pathways from the complete genome sequence
31. Recent developments and future directions in computational genomics
32. Errors in genome annotation
33. Errors in genome reviews
34. Some measures of comparative performance in the three CASPs
35. Intrinsic errors in genome annotation
36. Annotating eukaryotic genomes
37. Functional and structural genomics using PEDANT