Genome annotation assessment in Drosophila melanogaster.
Computational methods for automated genome annotation are critical to our community's ability to make full use of the large volume of genomic sequence being generated and released. To explore the accuracy of these automated feature prediction tools in the genomes of higher organisms, we evaluat...
| Autores: | , , , , , |
|---|---|
| Formato: | artículo |
| Estado: | Versión publicada |
| Fecha de publicación: | 2000 |
| País: | España |
| Recursos: | Universidad de Barcelona |
| Repositorio: | Dipòsit Digital de la UB |
| OAI Identifier: | oai:diposit.ub.edu:2445/192625 |
| Acesso em linha: | https://hdl.handle.net/2445/192625 |
| Access Level: | acceso abierto |
| Palavra-chave: | Drosòfila melanogaster Drosòfila Genòmica Drosophila melanogaster Drosophila Genomics |
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Genome annotation assessment in Drosophila melanogaster.Reese, Martin G.Hartzell, GeorgeHarris, Nomi L.Ohler, UweAbril Ferrando, Josep Francesc, 1970-Lewis, Suzanna E.Drosòfila melanogasterDrosòfilaGenòmicaDrosophila melanogasterDrosophilaGenomicsComputational methods for automated genome annotation are critical to our community's ability to make full use of the large volume of genomic sequence being generated and released. To explore the accuracy of these automated feature prediction tools in the genomes of higher organisms, we evaluated their performance on a large, well-characterized sequence contig from the Adh region ofDrosophila melanogaster. This experiment, known as the Genome Annotation Assessment Project (GASP), was launched in May 1999. Twelve groups, applying state-of-the-art tools, contributed predictions for features including gene structure, protein homologies, promoter sites, and repeat elements. We evaluated these predictions using two standards, one based on previously unreleased high-quality full-length cDNA sequences and a second based on the set of annotations generated as part of an in-depth study of the region by a group ofDrosophila experts. Although these standard sets only approximate the unknown distribution of features in this region, we believe that when taken in context the results of an evaluation based on them are meaningful. The results were presented as a tutorial at the conference on Intelligent Systems in Molecular Biology (ISMB-99) in August 1999. Over 95% of the coding nucleotides in the region were correctly identified by the majority of the gene finders, and the correct intron/exon structures were predicted for >40% of the genes. Homology-based annotation techniques recognized and associated functions with almost half of the genes in the region; the remainder were only identified by the ab initio techniques. This experiment also presents the first assessment of promoter prediction techniques for a significant number of genes in a large contiguous region. We discovered that the promoter predictors' high false-positive rates make their predictions difficult to use. Integrating gene finding and cDNA/EST alignments with promoter predictions decreases the number of false-positive classifications but discovers less than one-third of the promoters in the region. We believe that by establishing standards for evaluating genomic annotations and by assessing the performance of existing automated genome annotation tools, this experiment establishes a baseline that contributes to the value of ongoing large-scale annotation projects and should guide further research in genome informatics.Cold Spring Harbor Laboratory Press2000info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfhttps://hdl.handle.net/2445/192625Articles publicats en revistes (Genètica, Microbiologia i Estadística)reponame:Dipòsit Digital de la UBinstname:Universidad de BarcelonaInglésReproducció del document publicat a: https://doi.org/10.1101/gr.10.4.483Genome Research, 2000, vol. 10, num. 4, p. 483-501https://doi.org/10.1101/gr.10.4.483cc-by-nc (c) Reese, Martin G. et al., 2000https://creativecommons.org/licenses/by-nc/4.0/info:eu-repo/semantics/openAccessoai:diposit.ub.edu:2445/1926252026-05-27T06:46:51Z |
| dc.title.none.fl_str_mv |
Genome annotation assessment in Drosophila melanogaster. |
| title |
Genome annotation assessment in Drosophila melanogaster. |
| spellingShingle |
Genome annotation assessment in Drosophila melanogaster. Reese, Martin G. Drosòfila melanogaster Drosòfila Genòmica Drosophila melanogaster Drosophila Genomics |
| title_short |
Genome annotation assessment in Drosophila melanogaster. |
| title_full |
Genome annotation assessment in Drosophila melanogaster. |
| title_fullStr |
Genome annotation assessment in Drosophila melanogaster. |
| title_full_unstemmed |
Genome annotation assessment in Drosophila melanogaster. |
| title_sort |
Genome annotation assessment in Drosophila melanogaster. |
| dc.creator.none.fl_str_mv |
Reese, Martin G. Hartzell, George Harris, Nomi L. Ohler, Uwe Abril Ferrando, Josep Francesc, 1970- Lewis, Suzanna E. |
| author |
Reese, Martin G. |
| author_facet |
Reese, Martin G. Hartzell, George Harris, Nomi L. Ohler, Uwe Abril Ferrando, Josep Francesc, 1970- Lewis, Suzanna E. |
| author_role |
author |
| author2 |
Hartzell, George Harris, Nomi L. Ohler, Uwe Abril Ferrando, Josep Francesc, 1970- Lewis, Suzanna E. |
| author2_role |
author author author author author |
| dc.subject.none.fl_str_mv |
Drosòfila melanogaster Drosòfila Genòmica Drosophila melanogaster Drosophila Genomics |
| topic |
Drosòfila melanogaster Drosòfila Genòmica Drosophila melanogaster Drosophila Genomics |
| description |
Computational methods for automated genome annotation are critical to our community's ability to make full use of the large volume of genomic sequence being generated and released. To explore the accuracy of these automated feature prediction tools in the genomes of higher organisms, we evaluated their performance on a large, well-characterized sequence contig from the Adh region ofDrosophila melanogaster. This experiment, known as the Genome Annotation Assessment Project (GASP), was launched in May 1999. Twelve groups, applying state-of-the-art tools, contributed predictions for features including gene structure, protein homologies, promoter sites, and repeat elements. We evaluated these predictions using two standards, one based on previously unreleased high-quality full-length cDNA sequences and a second based on the set of annotations generated as part of an in-depth study of the region by a group ofDrosophila experts. Although these standard sets only approximate the unknown distribution of features in this region, we believe that when taken in context the results of an evaluation based on them are meaningful. The results were presented as a tutorial at the conference on Intelligent Systems in Molecular Biology (ISMB-99) in August 1999. Over 95% of the coding nucleotides in the region were correctly identified by the majority of the gene finders, and the correct intron/exon structures were predicted for >40% of the genes. Homology-based annotation techniques recognized and associated functions with almost half of the genes in the region; the remainder were only identified by the ab initio techniques. This experiment also presents the first assessment of promoter prediction techniques for a significant number of genes in a large contiguous region. We discovered that the promoter predictors' high false-positive rates make their predictions difficult to use. Integrating gene finding and cDNA/EST alignments with promoter predictions decreases the number of false-positive classifications but discovers less than one-third of the promoters in the region. We believe that by establishing standards for evaluating genomic annotations and by assessing the performance of existing automated genome annotation tools, this experiment establishes a baseline that contributes to the value of ongoing large-scale annotation projects and should guide further research in genome informatics. |
| publishDate |
2000 |
| dc.date.none.fl_str_mv |
2000 |
| dc.type.none.fl_str_mv |
info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion |
| format |
article |
| status_str |
publishedVersion |
| dc.identifier.none.fl_str_mv |
https://hdl.handle.net/2445/192625 |
| url |
https://hdl.handle.net/2445/192625 |
| dc.language.none.fl_str_mv |
Inglés |
| language_invalid_str_mv |
Inglés |
| dc.relation.none.fl_str_mv |
Reproducció del document publicat a: https://doi.org/10.1101/gr.10.4.483 Genome Research, 2000, vol. 10, num. 4, p. 483-501 https://doi.org/10.1101/gr.10.4.483 |
| dc.rights.none.fl_str_mv |
cc-by-nc (c) Reese, Martin G. et al., 2000 https://creativecommons.org/licenses/by-nc/4.0/ info:eu-repo/semantics/openAccess |
| rights_invalid_str_mv |
cc-by-nc (c) Reese, Martin G. et al., 2000 https://creativecommons.org/licenses/by-nc/4.0/ |
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openAccess |
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application/pdf |
| dc.publisher.none.fl_str_mv |
Cold Spring Harbor Laboratory Press |
| publisher.none.fl_str_mv |
Cold Spring Harbor Laboratory Press |
| dc.source.none.fl_str_mv |
Articles publicats en revistes (Genètica, Microbiologia i Estadística) reponame:Dipòsit Digital de la UB instname:Universidad de Barcelona |
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Universidad de Barcelona |
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Dipòsit Digital de la UB |
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Dipòsit Digital de la UB |
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