Genome annotation

Plant Physiology and Biochemistry

Volumn 39, Issue 3-4, 2001, Pages 181-193

  Aubourg, S ^a   Rouze P ^a  

^a GHENT UNIVERSITY   (Belgium)

Author keywords

Annotation; Arabidopsis; Bioinformatics; Database; Gene prediction; Genomics

Indexed keywords

DATA BASE; DIFFERENTIAL DISPLAY; GENE FUNCTION; GENE SEQUENCE; GENETIC REGULATION; INFORMATION PROCESSING; ONLINE ANALYSIS; PLANT GENOME;

ARABIDOPSIS THALIANA;

EID: 0035055145     PISSN: 09819428     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0981-9428(01)01242-6     Document Type: Review

References (85)

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2. In Arabidopsis thaliana, 1% of the genome codes for a novel protein family unique to plants
3. Structure, organization and putative function of the genes identified within a 23.9 kb fragment from Arabidopsis thaliana chromosome IV
4. GAIA: Framework annotation of genomic sequence
5. The distribution of genes in the genomes of Gramineae
6. Gene expression informatics - It's all in your mine
7. Human and mouse gene structure: Comparative analysis and application to exon prediction
8. Comparative sequence analysis of plant nuclear genomes: Microcolinearity and its many exceptions
9. Objective: The complete sequence of a plant genome
10. The small, the large and the wild: The value of comparison in plant genomics
11. Clearing a path through the jungle: Progress in Arabidopsis genomics
12. Extensive duplication and reshuffling in the Arabidopsis genome
13. dbEST-database for 'expressed sequence tags'
14. Predicting functions from protein sequences - Where are the bottlenecks?
15. Predicting function: From genes to genomes and back
16. GENMARK: Parallel gene recognition for both DNA strands
17. Intrinsic and extrinsic approaches for detecting genes in a bacterial genome
18. Functional genomics in plants
19. Prediction of splice sites in plant pre-mRNA from sequence properties
20. Errors in genome annotation
21. Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships
22. Prediction of complete gene structures in human genomic DNA
23. Finding the genes in genomic DNA
24. Codon usage as a tool to predict the cellular location of eukaryotic ribosomal proteins and aminoacyl-tRNA synthetases
25. Computational methods for the identification of genes in vertebrate genomes sequences
26. Do we need a huge new center to annotate the human genome?
27. The evolution of plant nuclear genes
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29. The Delphic boat or what the genomic texts tell us
30. Plant genome databases: From references to inferences tools
31. Predicting subcellular localization of proteins based on their N-terminal amino acid sequence
32. ESTs reveal a multigene family for plant defensins in Arabidopsis thaliana
33. Identifying potential tRNA genes in genomic DNA sequences
34. The gene identification problem: An overview for developer
35. Using metabolic pathway databases for functional annotation
36. Sources of systematic error in functional annotation of genomes: Domain rearrangement, non-orthologous gene displacement, and operon disruption
37. Rice as a model for cereal genomics
38. In silico detection of control signals: mRNA 3′-end-processing sequences in diverse species
39. Splice site prediction in Arabidopsis thaliana pre mRNA by combining local and global sequence information
40. Gene families: The taxonomy of protein paralogs and chimeras
41. A tool for analyzing and annotating genomic sequences
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43. Exploitation of gene context
44. Protein structure prediction in the postgenomic area
45. From genome to functional genomics
46. Isolation and analysis of cDNA within a 300 kb Arabidopsis thaliana genomic region located around the 100 map unit of chromosome 1
47. Genomes OnLine Database (GOLD): A monitor of complete and ongoing genome projects world wide
48. Whole-genome sequence annotation: 'Going wrong with confidence'
49. Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana
50. Genomics, gene expression and DNA arrays
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52. GeneMark.hmm: New solutions for gene finding
53. A combined algorithm for genome-wide prediction of protein function
54. The mitochondrial genome of Arabidopsis is composed of both native and immigrant information
55. Gene prediction and gene classes in Arabidopsis thaliana
56. Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana
57. The complete sequence of a heterochromatic island from a higher eukaryote
58. Imagene: An integrated computer environment for sequence annotation and analysis
59. Overview of the yeast genome
60. The role of the genome project in determining gene function: Insights from model organisms
61. A contiguous 60 kb genomic stretch from barley reveals molecular evidence for gene islands in a monocot genome
62. Evaluation of gene prediction software using a genomic data set: Application to Arabidopsis thaliana sequences
63. Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles
64. The TIGR Gene Indices: Reconstruction and representation of expressed gene sequences
65. Differential methylation of genes and retrotransposons facilitates shotgun sequencing of the maize genome
66. High-throughput functional annotation of novel genes products using document clustering
67. PlantCARE, a cis-acting regulatory element database
68. Large-scale sequencing of plant genomes
69. Genome annotation: Which tools do we have for it?
70. International Rice Genome Sequencing Project: The effort to completely sequence the rice genome
71. Complete structure of the chloroplast genome of Arabidopsis thaliana
72. Structural analysis of Arabidopsis thaliana chromosome 3. Sequence features of the region of 4,504,864 bp covered by sixty P1 and TAC clones
73. The challenges of genome sequence annotation or 'The devil is in the details'
74. A genomic perspective on protein families
75. Organization and structural evolution of four multigene families in Arabidopsis thaliana: AtLCAD, AtLGT, AtMYST and AtHD-GL2
76. Evidence for an ancient chromosomal duplication in Arabidopsis thaliana by sequencing and analyzing a 400-kb contig at the APETALA2 locus on chromosome 4
77. A probabilistic model for detecting coding regions in DNA sequences
78. A branch point consensus from Arabidopsis found by non circular analysis allows for better prediction of acceptor sites
79. Progress in Arabidopsis genome sequencing and functional genomics
80. Late-night thoughts on the sequence annotation problem
81. Of genes and genomes and the origin of maize
82. Automated gene identification in large-scale genomic sequences
83. Mass spectrometry and the age of the proteome
84. Identification of protein coding regions in the human genome by quadratic discriminant analysis