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Literature DB >> 10779496

Using GeneWise in the Drosophila annotation experiment.

Abstract

The GeneWise method for combining gene prediction and homology searches was applied to the 2.9-Mb region from Drosophila melanogaster. The results from the Genome Annotation Assessment Project (GASP) showed that GeneWise provided reasonably accurate gene predictions. Further investigation indicates that many of the incorrect gene predictions from GeneWise were due to transposons with valid protein-coding genes and the remaining cases are pseudogenes or possible annotation oversights.

Entities: Species

Mesh：

Year: 2000 PMID： 10779496 PMCID： PMC310858 DOI： 10.1101/gr.10.4.547

Source DB: PubMed Journal: Genome Res ISSN： 1088-9051 Impact factor: 9.043

9 in total

1. Critical assessment of methods of protein structure prediction (CASP): round III.

Authors: J Moult; T Hubbard; K Fidelis; J T Pedersen
Journal: Proteins Date: 1999

2. The Pfam protein families database.

Authors: A Bateman; E Birney; R Durbin; S R Eddy; K L Howe; E L Sonnhammer
Journal: Nucleic Acids Res Date: 2000-01-01 Impact factor: 16.971

Review 3. Profile hidden Markov models.

Authors: S R Eddy
Journal: Bioinformatics Date: 1998 Impact factor: 6.937

4. Two methods for improving performance of an HMM and their application for gene finding.

Authors: A Krogh
Journal: Proc Int Conf Intell Syst Mol Biol Date: 1997

5. Discovering and understanding genes in human DNA sequence using GRAIL.

Authors: E C Uberbacher; Y Xu; R J Mural
Journal: Methods Enzymol Date: 1996 Impact factor: 1.600

6. A generalized hidden Markov model for the recognition of human genes in DNA.

Authors: D Kulp; D Haussler; M G Reese; F H Eeckman
Journal: Proc Int Conf Intell Syst Mol Biol Date: 1996

7. Genome annotation assessment in Drosophila melanogaster.

Authors: M G Reese; G Hartzell; N L Harris; U Ohler; J F Abril; S E Lewis
Journal: Genome Res Date: 2000-04 Impact factor: 9.043

8. Prediction of complete gene structures in human genomic DNA.

Authors: C Burge; S Karlin
Journal: J Mol Biol Date: 1997-04-25 Impact factor: 5.469

9. Hidden Markov models in computational biology. Applications to protein modeling.

Authors: A Krogh; M Brown; I S Mian; K Sjölander; D Haussler
Journal: J Mol Biol Date: 1994-02-04 Impact factor: 5.469

9 in total

152 in total

1. Massive sequence comparisons as a help in annotating genomic sequences.

Authors: A Louis; E Ollivier; J C Aude; J L Risler
Journal: Genome Res Date: 2001-07 Impact factor: 9.043

2. The Ensembl genome database project.

Authors: T Hubbard; D Barker; E Birney; G Cameron; Y Chen; L Clark; T Cox; J Cuff; V Curwen; T Down; R Durbin; E Eyras; J Gilbert; M Hammond; L Huminiecki; A Kasprzyk; H Lehvaslaiho; P Lijnzaad; C Melsopp; E Mongin; R Pettett; M Pocock; S Potter; A Rust; E Schmidt; S Searle; G Slater; J Smith; W Spooner; A Stabenau; J Stalker; E Stupka; A Ureta-Vidal; I Vastrik; M Clamp
Journal: Nucleic Acids Res Date: 2002-01-01 Impact factor: 16.971

Using GeneWise in the Drosophila annotation experiment.

1. Critical assessment of methods of protein structure prediction (CASP): round III.

2. The Pfam protein families database.

Review 3. Profile hidden Markov models.

4. Two methods for improving performance of an HMM and their application for gene finding.

5. Discovering and understanding genes in human DNA sequence using GRAIL.

6. A generalized hidden Markov model for the recognition of human genes in DNA.

7. Genome annotation assessment in Drosophila melanogaster.

8. Prediction of complete gene structures in human genomic DNA.

9. Hidden Markov models in computational biology. Applications to protein modeling.

1. Massive sequence comparisons as a help in annotating genomic sequences.

2. The Ensembl genome database project.

3. A nutrient-regulated, dual localization phospholipase A(2) in the symbiotic fungus Tuber borchii.

4. DIAN: a novel algorithm for genome ontological classification.

5. Computational inference of homologous gene structures in the human genome.

6. SLAM: cross-species gene finding and alignment with a generalized pair hidden Markov model.

Review 7. Chlamydomonas reinhardtii at the crossroads of genomics.

8. Gene structure prediction in syntenic DNA segments.

9. Comparative genomic analysis in the region of a major Plasmodium-refractoriness locus of Anopheles gambiae.

10. Birth of a new gene on the Y chromosome of Drosophila melanogaster.