An assessment of gene prediction accuracy in large DNA sequences
One of the first useful products from the human genome will be a set of predicted genes. Besides its intrinsic scientific interest, the accuracy and completeness of this data set is of considerable importance for human health and medicine. Though progress has been made on computational gene identifi...
| Autores: | , , , , |
|---|---|
| Tipo de recurso: | artículo |
| Estado: | Versión publicada |
| Fecha de publicación: | 2000 |
| País: | España |
| Institución: | Universidad de Barcelona |
| Repositorio: | Dipòsit Digital de la UB |
| OAI Identifier: | oai:diposit.ub.edu:2445/192700 |
| Acceso en línea: | https://hdl.handle.net/2445/192700 |
| Access Level: | acceso abierto |
| Palabra clave: | ADN Genoma humà Seqüència de nucleòtids Genètica humana DNA Human genome Nucleotide sequence Human genetics |
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An assessment of gene prediction accuracy in large DNA sequencesGuigó, RodericAgarwal, PankajAbril Ferrando, Josep Francesc, 1970-Burset Albareda, MoisèsFickett, J.W.ADNGenoma humàSeqüència de nucleòtidsGenètica humanaDNAHuman genomeNucleotide sequenceHuman geneticsOne of the first useful products from the human genome will be a set of predicted genes. Besides its intrinsic scientific interest, the accuracy and completeness of this data set is of considerable importance for human health and medicine. Though progress has been made on computational gene identification in terms of both methods and accuracy evaluation measures, most of the sequence sets in which the programs are tested are short genomic sequences, and there is concern that these accuracy measures may not extrapolate well to larger, more challenging data sets. Given the absence of experimentally verified large genomic data sets, we constructed a semiartificial test set comprising a number of short single-gene genomic sequences with randomly generated intergenic regions. This test set, which should still present an easier problem than real human genomic sequence, mimics the ∼200kb long BACs being sequenced. In our experiments with these longer genomic sequences, the accuracy ofGENSCAN, one of the most accurate ab initio gene prediction programs, dropped significantly, although its sensitivity remained high. Conversely, the accuracy of similarity-based programs, such as GENEWISE,PROCRUSTES, andBLASTX, was not affected significantly by the presence of random intergenic sequence, but depended on the strength of the similarity to the protein homolog. As expected, the accuracy dropped if the models were built using more distant homologs, and we were able to quantitatively estimate this decline. However, the specificities of these techniques are still rather good even when the similarity is weak, which is a desirable characteristic for driving expensive follow-up experiments. Our experiments suggest that though gene prediction will improve with every new protein that is discovered and through improvements in the current set of tools, we still have a long way to go before we can decipher the precise exonic structure of every gene in the human genome using purely computational methodology.Cold Spring Harbor Laboratory Press2000info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfhttps://hdl.handle.net/2445/192700Articles 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.143200Genome Research, 2000, vol. 10, num. 10, p. 1631-1642https://doi.org/10.1101/gr.143200cc-by-nc (c) Guigó, Roderic et al., 2000https://creativecommons.org/licenses/by-nc/4.0/info:eu-repo/semantics/openAccessoai:diposit.ub.edu:2445/1927002026-05-27T06:46:51Z |
| dc.title.none.fl_str_mv |
An assessment of gene prediction accuracy in large DNA sequences |
| title |
An assessment of gene prediction accuracy in large DNA sequences |
| spellingShingle |
An assessment of gene prediction accuracy in large DNA sequences Guigó, Roderic ADN Genoma humà Seqüència de nucleòtids Genètica humana DNA Human genome Nucleotide sequence Human genetics |
| title_short |
An assessment of gene prediction accuracy in large DNA sequences |
| title_full |
An assessment of gene prediction accuracy in large DNA sequences |
| title_fullStr |
An assessment of gene prediction accuracy in large DNA sequences |
| title_full_unstemmed |
An assessment of gene prediction accuracy in large DNA sequences |
| title_sort |
An assessment of gene prediction accuracy in large DNA sequences |
| dc.creator.none.fl_str_mv |
Guigó, Roderic Agarwal, Pankaj Abril Ferrando, Josep Francesc, 1970- Burset Albareda, Moisès Fickett, J.W. |
| author |
Guigó, Roderic |
| author_facet |
Guigó, Roderic Agarwal, Pankaj Abril Ferrando, Josep Francesc, 1970- Burset Albareda, Moisès Fickett, J.W. |
| author_role |
author |
| author2 |
Agarwal, Pankaj Abril Ferrando, Josep Francesc, 1970- Burset Albareda, Moisès Fickett, J.W. |
| author2_role |
author author author author |
| dc.subject.none.fl_str_mv |
ADN Genoma humà Seqüència de nucleòtids Genètica humana DNA Human genome Nucleotide sequence Human genetics |
| topic |
ADN Genoma humà Seqüència de nucleòtids Genètica humana DNA Human genome Nucleotide sequence Human genetics |
| description |
One of the first useful products from the human genome will be a set of predicted genes. Besides its intrinsic scientific interest, the accuracy and completeness of this data set is of considerable importance for human health and medicine. Though progress has been made on computational gene identification in terms of both methods and accuracy evaluation measures, most of the sequence sets in which the programs are tested are short genomic sequences, and there is concern that these accuracy measures may not extrapolate well to larger, more challenging data sets. Given the absence of experimentally verified large genomic data sets, we constructed a semiartificial test set comprising a number of short single-gene genomic sequences with randomly generated intergenic regions. This test set, which should still present an easier problem than real human genomic sequence, mimics the ∼200kb long BACs being sequenced. In our experiments with these longer genomic sequences, the accuracy ofGENSCAN, one of the most accurate ab initio gene prediction programs, dropped significantly, although its sensitivity remained high. Conversely, the accuracy of similarity-based programs, such as GENEWISE,PROCRUSTES, andBLASTX, was not affected significantly by the presence of random intergenic sequence, but depended on the strength of the similarity to the protein homolog. As expected, the accuracy dropped if the models were built using more distant homologs, and we were able to quantitatively estimate this decline. However, the specificities of these techniques are still rather good even when the similarity is weak, which is a desirable characteristic for driving expensive follow-up experiments. Our experiments suggest that though gene prediction will improve with every new protein that is discovered and through improvements in the current set of tools, we still have a long way to go before we can decipher the precise exonic structure of every gene in the human genome using purely computational methodology. |
| 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 |
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article |
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publishedVersion |
| dc.identifier.none.fl_str_mv |
https://hdl.handle.net/2445/192700 |
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https://hdl.handle.net/2445/192700 |
| 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.143200 Genome Research, 2000, vol. 10, num. 10, p. 1631-1642 https://doi.org/10.1101/gr.143200 |
| dc.rights.none.fl_str_mv |
cc-by-nc (c) Guigó, Roderic et al., 2000 https://creativecommons.org/licenses/by-nc/4.0/ info:eu-repo/semantics/openAccess |
| rights_invalid_str_mv |
cc-by-nc (c) Guigó, Roderic 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 |
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Cold Spring Harbor Laboratory Press |
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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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