ASPic-GeneID: a lightweight pipeline for gene prediction and alternative isoforms detection

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• dc.contributor.author Alioto, Tylerca
• dc.contributor.author Picardi, Ernestoca
• dc.contributor.author Guigó Serra, Rodericca
• dc.contributor.author Pesole, Grazianoca
• dc.date.accessioned 2014-06-20T08:17:59Z
• dc.date.available 2014-06-20T08:17:59Z
• dc.date.issued 2013ca
• dc.description.abstract New genomes are being sequenced at an increasingly rapid rate, far outpacing the rate at which manual gene annotation can be performed. Automated genome annotation is thus necessitated by this growth in genome projects; however, full-fledged annotation systems are usually home-grown and customized to a particular genome. There is thus a renewed need for accurate ab initio gene prediction methods. However, it is apparent that fully ab initio methods fall short of the required level of sensitivity and specificity for a quality annotation. Evidence in the form of expressed sequences gives the single biggest improvement in accuracy when used to inform gene predictions. Here, we present a lightweight pipeline for first-pass gene prediction on newly sequenced genomes. The two main components are ASPic, a program that derives highly accurate, albeit not necessarily complete, EST-based transcript annotations from EST alignments, and GeneID, a standard gene prediction program, which we have modified to take as evidence intron annotations. The introns output by ASPic CDS predictions is given to GeneID to constrain the exon-chaining process and produce predictions consistent with the underlying EST alignments. The pipeline was successfully tested on the entire C. elegans genome and the 44 ENCODE human pilot regions.
• dc.description.sponsorship This work was supported by the Italian Ministero dell’Istruzione, Università e Ricerca (MIUR): PRIN 2009 and 2010; Consiglio Nazionale delle Ricerche: Flagship Project Epigen, Aging Program2012–2014, and by the Italian Ministry for Foreign Affairs (Italy-Israel actions)
• dc.format.mimetype application/pdfca
• dc.identifier.citation Alioto T, Picardi E, Guigó R, Pesole G. ASPic-GeneID: a lightweight pipeline for gene prediction and alternative isoforms detection. Biomed Res Int. 2013;2013:502827. DOI: 10.1155/2013/502827ca
• dc.identifier.doi http://dx.doi.org/10.1155/2013/502827
• dc.identifier.issn 2314-6133ca
• dc.identifier.uri http://hdl.handle.net/10230/22587
• dc.language.iso engca
• dc.publisher Hindawica
• dc.relation.ispartof BioMed Research International. 2013;2013:502827
• dc.rights © 2013 Tyler Alioto et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly citedca
• dc.rights.accessRights info:eu-repo/semantics/openAccessca
• dc.rights.uri http://creativecommons.org/licenses/by/3.0/
• dc.subject.other Biologia computacional -- Mètodes
• dc.subject.other Genòmica
• dc.title ASPic-GeneID: a lightweight pipeline for gene prediction and alternative isoforms detectionca
• dc.type info:eu-repo/semantics/articleca
• dc.type.version info:eu-repo/semantics/publishedVersionca