Comparative gene prediction in human and mouse

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Parra G, Agarwal P, Abril JF, Wiehe T, Fickett JW, Guigó R. Comparative gene prediction in human and mouse. Genome Res. 2003; 13(1): 108-17. DOI: 10.1101/gr.871403
http://hdl.handle.net/10230/16484
To cite or link this document: http://hdl.handle.net/10230/16484
dc.contributor.author Parra Farré, Genís
dc.contributor.author Agarwal, Pankaj
dc.contributor.author Abril Ferrando, Josep Francesc
dc.contributor.author Wiehe, Thomas
dc.contributor.author Fickett, James W.
dc.contributor.author Guigó Serra, Roderic
dc.date.accessioned 2012-05-24T14:28:20Z
dc.date.available 2012-05-24T14:28:20Z
dc.date.issued 2003
dc.identifier.citation Parra G, Agarwal P, Abril JF, Wiehe T, Fickett JW, Guigó R. Comparative gene prediction in human and mouse. Genome Res. 2003; 13(1): 108-17. DOI: 10.1101/gr.871403
dc.identifier.issn 1088-9051
dc.identifier.uri http://hdl.handle.net/10230/16484
dc.description.abstract The completion of the sequencing of the mouse genome promises to help predict human genes with greater accuracy. While current ab initio gene prediction programs are remarkably sensitive (i.e., they predict at least a fragment of most genes), their specificity is often low, predicting a large number of false-positive genes in the human genome. Sequence conservation at the protein level with the mouse genome can help eliminate some of those false positives. Here we describe SGP2, a gene prediction program that combines ab initio gene prediction with TBLASTX searches between two genome sequences to provide both sensitive and specific gene predictions. The accuracy of SGP2 when used to predict genes by comparing the human and mouse genomes is assessed on a number of data sets, including single-gene data sets, the highly curated human chromosome 22 predictions, and entire genome predictions from ENSEMBL. Results indicate that SGP2 outperforms purely ab initio gene prediction methods. Results also indicate that SGP2 works about as well with 3x shotgun data as it does with fully assembled genomes. SGP2 provides a high enough specificity that its predictions can be experimentally verified at a reasonable cost. SGP2 was used to generate a complete set of gene predictions on both the human and mouse by comparing the genomes of these two species. Our results suggest that another few thousand human and mouse genes currently not in ENSEMBL are worth verifying experimentally.
dc.language.iso eng
dc.publisher Cold Spring Harbor Laboratory Press-CSHL Press
dc.relation.ispartof Genome Res. 2003; 13(1): 108-17
dc.rights © 2003 Genome Research by Cold Spring Harbor Laboratory Press. Published version available at http://genome.cshlp.org. Aquest document està subjecte a Llicència Creative Commons (Attribution-NonCommercial 3.0 Unported License)
dc.rights.uri http://creativecommons.org/licenses/by-nc/3.0/
dc.subject.other Seqüències de nucleòtids
dc.subject.other Gens -- Identificació
dc.subject.other Genomes -- Anàlisi
dc.title Comparative gene prediction in human and mouse
dc.type info:eu-repo/semantics/article
dc.identifier.doi http://dx.doi.org/10.1101/gr.871403
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.type.version info:eu-repo/semantics/publishedVersion


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