Avaliação de Desempenho em Bioinformática: Estudo de caso de sistemas computacionais para a investigação de microRNAs
Resumo
Este artigo apresenta em detalhes a avaliação do sistema web miRQuest (http://mirquest.integrativebioinformatics.me/) que foi implementado e fez a integração dos principais preditores de microRNAs (miRNAs) em uma arquitetura de middleware, aplicado em um estudo com de caso em bioinformática.
Referências
Allmer J1, Yousef M. Computational methods for ab initio detection of microRNAs. Front Genet. 2012 Oct 10; 3:209. doi: 10.3389/fgene.2012.00209. eCollection 2012.
Araújo DAM, Maracaja-Coutinho V, Padilha IQM, Rego TG. (2005) Genômica e Bioinformática: importância e perspectivas para o Nordeste. Ciência e Cotidiano. 1:5-9.
Barros-Carvalho GA, Paschoal AR, Marcelino-Guimarães FC, Hungria M. (2014) Prediction of potential novel microRNAs in soybean when in symbiosis. Genet Mol Res. 13(4):8519-29. doi: 10.4238/2014.October.20.28.
Brameier M, Wiuf C (2007). Ab initio identification of human microRNAs based on structure motifs. BMC Bioinformatics, 8:478.
Gomes CP1, Cho JH, Hood L, Franco OL, Pereira RW, Wang K. (2013) A Review of Computational Tools in microRNA Discovery. Front Genet. 15; 4:81. doi: 10.3389/fgene.2013.00081.
Janssen S. et. al. (2008). Shape based indexing for faster search of RNA family databases. BMC Bioinformatics, 9:131.
Jiang P. et. al. (2007). MiPred: classification of real and pseudo microRNA precursors using random forest prediction model with combined features. Nucleic Acids, 35:339-344.
Kadri S. et al. (2009) HHMMiR: efficient de novo prediction of microRNAs using hierarchical hidden Markov models. BMC Bioinformatics. 10 Suppl 1:S35.
Kozomara A. and Griffiths-Jones S. (2014) miRBase: annotating high confidence microRNAs using deep sequencing data. NAR 42: D68-D73
Lee RC, Feinbaum RL, Ambros V; Feinbaum; Ambros (1993). "The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14". Cell 75 (5): 843–54. Doi: 10.1016/0092-8674(93)90529-Y. PMID 8252621.
Machado-Lima, A.; del Portillo, H.A. ; DURHAM, A.M. (2008) Computational methods in noncoding RNA research. Journal of Mathematical Biology, v. 56, p. 15-49.
Oliveira KC, Carvalho MLP, Maracaja-Coutinho V, Kitajima JP, Verjovski-Almeida S (2011). Non-coding RNAs in schistosomes: an unexplored world. Anais da Academia Brasileira de Ciências, 83(2): 673-694.
Padilha IQM, Durbano JPM, Martins AB, Almeida RS, Maracaja-Coutinho V, Araújo DAM. (2008) A bioinformática como instrumento de inserção digital e difusão da biotecnologia. Revista Eletrônica Extensão Cidadã, 5.
Paschoal AR, Maracaja-Coutinho V, Setubal JC, Simões ZL, Verjovski-Almeida S, Durham AM. (2012) Non-coding transcription characterization and annotation: A guide and web resource for non-coding RNA databases. RNA BIOL, 9:274-282.
Powers, D. M.W. (2011) Evaluation: From Precision, Recall and F-Measure to ROC, Informedness, Markedness e Correlation. Journal of Machine Learning Technologies, 2 (1) 37-63.
Severino P, Oliveira LS, Torres N, Andreghetto FM, Klingbeil Mde F, Moyses R, Wünsch-Filho V, Nunes FD, Mathor MB, Paschoal AR, Durham AM. (2013) High-throughput sequencing of small RNA transcriptomes reveals critical biological features targeted by microRNAs in cell models used for squamous cell cancer research. BMC Genomics. 14:735. doi: 10.1186/1471-2164-14-735.
Steffen P. et al. (2006) RNAshapes: an integrated RNA analysis package based on abstract shapes. Bioinformatics. 22(4):500-3.
Taft RJ, Pheasant M, Mattick JS. (2007). The relationship between non-protein-coding DNA and eukaryotic complexity. Bioessays. 29(3):288-99.
Teune J.-H. and Steger, G. (2010) NOVOMIR: De Novo Prediction of MicroRNA-Coding Regions in a Single Plant-Genome. Journal of Nucleic Acids.
Xue C. et al. (2005) Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine. BMC Bioinformatics, 6:310.
Zhang, B. et al. (2007) MicroRNAs and their regulatory roles in animals and plants. J. Cell. Physiol., 210:279–289.
Araújo DAM, Maracaja-Coutinho V, Padilha IQM, Rego TG. (2005) Genômica e Bioinformática: importância e perspectivas para o Nordeste. Ciência e Cotidiano. 1:5-9.
Barros-Carvalho GA, Paschoal AR, Marcelino-Guimarães FC, Hungria M. (2014) Prediction of potential novel microRNAs in soybean when in symbiosis. Genet Mol Res. 13(4):8519-29. doi: 10.4238/2014.October.20.28.
Brameier M, Wiuf C (2007). Ab initio identification of human microRNAs based on structure motifs. BMC Bioinformatics, 8:478.
Gomes CP1, Cho JH, Hood L, Franco OL, Pereira RW, Wang K. (2013) A Review of Computational Tools in microRNA Discovery. Front Genet. 15; 4:81. doi: 10.3389/fgene.2013.00081.
Janssen S. et. al. (2008). Shape based indexing for faster search of RNA family databases. BMC Bioinformatics, 9:131.
Jiang P. et. al. (2007). MiPred: classification of real and pseudo microRNA precursors using random forest prediction model with combined features. Nucleic Acids, 35:339-344.
Kadri S. et al. (2009) HHMMiR: efficient de novo prediction of microRNAs using hierarchical hidden Markov models. BMC Bioinformatics. 10 Suppl 1:S35.
Kozomara A. and Griffiths-Jones S. (2014) miRBase: annotating high confidence microRNAs using deep sequencing data. NAR 42: D68-D73
Lee RC, Feinbaum RL, Ambros V; Feinbaum; Ambros (1993). "The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14". Cell 75 (5): 843–54. Doi: 10.1016/0092-8674(93)90529-Y. PMID 8252621.
Machado-Lima, A.; del Portillo, H.A. ; DURHAM, A.M. (2008) Computational methods in noncoding RNA research. Journal of Mathematical Biology, v. 56, p. 15-49.
Oliveira KC, Carvalho MLP, Maracaja-Coutinho V, Kitajima JP, Verjovski-Almeida S (2011). Non-coding RNAs in schistosomes: an unexplored world. Anais da Academia Brasileira de Ciências, 83(2): 673-694.
Padilha IQM, Durbano JPM, Martins AB, Almeida RS, Maracaja-Coutinho V, Araújo DAM. (2008) A bioinformática como instrumento de inserção digital e difusão da biotecnologia. Revista Eletrônica Extensão Cidadã, 5.
Paschoal AR, Maracaja-Coutinho V, Setubal JC, Simões ZL, Verjovski-Almeida S, Durham AM. (2012) Non-coding transcription characterization and annotation: A guide and web resource for non-coding RNA databases. RNA BIOL, 9:274-282.
Powers, D. M.W. (2011) Evaluation: From Precision, Recall and F-Measure to ROC, Informedness, Markedness e Correlation. Journal of Machine Learning Technologies, 2 (1) 37-63.
Severino P, Oliveira LS, Torres N, Andreghetto FM, Klingbeil Mde F, Moyses R, Wünsch-Filho V, Nunes FD, Mathor MB, Paschoal AR, Durham AM. (2013) High-throughput sequencing of small RNA transcriptomes reveals critical biological features targeted by microRNAs in cell models used for squamous cell cancer research. BMC Genomics. 14:735. doi: 10.1186/1471-2164-14-735.
Steffen P. et al. (2006) RNAshapes: an integrated RNA analysis package based on abstract shapes. Bioinformatics. 22(4):500-3.
Taft RJ, Pheasant M, Mattick JS. (2007). The relationship between non-protein-coding DNA and eukaryotic complexity. Bioessays. 29(3):288-99.
Teune J.-H. and Steger, G. (2010) NOVOMIR: De Novo Prediction of MicroRNA-Coding Regions in a Single Plant-Genome. Journal of Nucleic Acids.
Xue C. et al. (2005) Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine. BMC Bioinformatics, 6:310.
Zhang, B. et al. (2007) MicroRNAs and their regulatory roles in animals and plants. J. Cell. Physiol., 210:279–289.
Publicado
20/07/2015
Como Citar
AGUIAR, Rosana; AMBROSIO, Leandro; SEPÚLVEDA-HERMOSILLA, Gonzalo; MARACAJA-COUTINHO, Vinicius; PASCHOAL, Alexandre.
Avaliação de Desempenho em Bioinformática: Estudo de caso de sistemas computacionais para a investigação de microRNAs. In: WORKSHOP EM DESEMPENHO DE SISTEMAS COMPUTACIONAIS E DE COMUNICAÇÃO (WPERFORMANCE), 14. , 2015, Recife.
Anais [...].
Porto Alegre: Sociedade Brasileira de Computação,
2015
.
p. 202-206.
ISSN 2595-6167.
DOI: https://doi.org/10.5753/wperformance.2015.10413.
