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https://hdl.handle.net/1822/61324
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Campo DC | Valor | Idioma |
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dc.contributor.author | Cruz, Fernando João Pereira da | por |
dc.contributor.author | Lagoa, Davide Rafael Santos | por |
dc.contributor.author | Mendes, João | por |
dc.contributor.author | Rocha, I. | por |
dc.contributor.author | Ferreira, Eugénio C. | por |
dc.contributor.author | Rocha, Miguel | por |
dc.contributor.author | Dias, Oscar | por |
dc.date.accessioned | 2019-09-06T10:28:01Z | - |
dc.date.available | 2019-09-06T10:28:01Z | - |
dc.date.issued | 2019-09-05 | - |
dc.identifier.citation | Cruz, Fernado; Lagoa, D.; Mendes, João; Rocha, Isabel; Ferreira, Eugénio C.; Rocha, Miguel; Dias, Oscar, SamPler - a novel method for selecting parameters for gene functional annotation routines. BMC Bioinformatics, 20(454), 2019 | por |
dc.identifier.issn | 1471-2105 | por |
dc.identifier.uri | https://hdl.handle.net/1822/61324 | - |
dc.description.abstract | Background: As genome sequencing projects grow rapidly, the diversity of organisms with recently assembled genome sequences peaks at an unprecedented scale, thereby highlighting the need to make gene functional annotations fast and efficient. However, the (high) quality of such annotations must be guaranteed, as this is the first indicator of the genomic potential of every organism. Automatic procedures help accelerating the annotation process, though decreasing the confidence and reliability of the outcomes. Manually curating a genome-wide annotation of genes, enzymes and transporter proteins function is a highly time-consuming, tedious and impractical task, even for the most proficient curator. Hence, a semi-automated procedure, which balances the two approaches, will increase the reliability of the annotation, while speeding up the process. In fact, a prior analysis of the annotation algorithm may leverage its performance, by manipulating its parameters, hastening the downstream processing and the manual curation of assigning functions to genes encoding proteins. Results: Here SamPler, a novel strategy to select parameters for gene functional annotation routines is presented. This semi-automated method is based on the manual curation of a randomly selected set of genes/proteins. Then, in a multi-dimensional array, this sample is used to assess the automatic annotations for all possible combinations of the algorithm’s parameters. These assessments allow creating an array of confusion matrices, for which several metrics are calculated (accuracy, precision and negative predictive value) and used to reach optimal values for the parameters. Conclusions: The potential of this methodology is demonstrated with four genome functional annotations performed in merlin, an in-house user-friendly computational framework for genome-scale metabolic annotation and model reconstruction. For that, SamPler was implemented as a new plugin for the merlin tool. | por |
dc.description.sponsorship | This study was supported by the Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding of [UID/BIO/ 04469] unit and COMPETE 2020 [POCI-01-0145-FEDER-006684] and BioTecNorte operation [NORTE-01-0145-FEDER-000004] funded by the European Regional Development Fund under the scope of Norte2020 - Programa Operacional Regional do Norte. The authors thank the project DDDeCaF - Bioinformatics Services for Data-Driven Design of Cell Factories and Communities, Ref. H2020-LEIT-BIO-2015-1 686070–1, funded by the European Commission. | por |
dc.language.iso | eng | por |
dc.publisher | Springer Nature | por |
dc.relation | info:eu-repo/grantAgreement/FCT/5876/147337/PT | por |
dc.rights | openAccess | por |
dc.subject | SamPler | por |
dc.subject | Annotation routines | por |
dc.subject | Parametrization | por |
dc.subject | Merlin | por |
dc.title | SamPler - a novel method for selecting parameters for gene functional annotation routines | por |
dc.type | article | - |
dc.peerreviewed | yes | por |
dc.relation.publisherversion | http://www.biomedcentral.com/bmcbioinformatics | por |
dc.comments | CEB51971 | por |
oaire.citationStartPage | 1 | por |
oaire.citationEndPage | 11 | por |
oaire.citationIssue | 1 | por |
oaire.citationVolume | 20 | por |
dc.date.updated | 2019-09-06T09:33:44Z | - |
dc.identifier.eissn | 1471-2105 | por |
dc.identifier.doi | 10.1186/s12859-019-3038-4 | por |
dc.identifier.pmid | 31488049 | por |
dc.description.publicationversion | info:eu-repo/semantics/publishedVersion | - |
dc.subject.wos | Science & Technology | por |
sdum.journal | BMC Bioinformatics | por |
Aparece nas coleções: | CEB - Publicações em Revistas/Séries Internacionais / Publications in International Journals/Series |
Ficheiros deste registo:
Ficheiro | Descrição | Tamanho | Formato | |
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document_51971_1.pdf | 1,72 MB | Adobe PDF | Ver/Abrir |