Abstract
RNA genes are unquestionable today, non-coding RNA is functional but its classification at the present is complex due to lack of computational tools. The vast progress in computer science for DNA and protein is not enough to resolve folding and function of RNA. Fortunately, computational tools for solving RNA concerns are in progress: web source as Centroid Homofold, CentroidFold (CBRC), Rfam (Sanger-HHMI, Janelia farm), sRNAdb (MGIL), RNApredator (Vienna RNA web server), TargetRNA2 (Wellesley College), Noncoding RNAdatabase (IBC), Mfold (CAS) and RNAcon (IMTC) are quickly supplying the bioinformatics gaps. In this work was used those tools to fill and appoint the intergenic annotation in the Leuconostoc mesenteroides bacterium, recently sequenced in 454 Roche. More than 2000 intergenic sequence were run on the mentioned tools. Various ncRNA were classified as Mir-(#)s, many T-Boxes, various L(#) leaders and some ones TPPs, yybp-ykoY and ykkC-yxkD, between others. Other interesting structures without matching in Rfam, ncRNA databases were annotated as hypothetical ncRNA.
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References
Hamada, M., Sato, K., Kiryu, H., Mituyama, T., Asai, K.: Predictions of RNA secondary structure by combining homologous sequence information. Bioinformatics 25(12), i330–i338 (2009)
Hershberg, R., Altuvia, S., Margalit, H.: A survey of small RNA-encoding genes in Escherichia coli. Nucleic Acids Res. 31, 1813–1820 (2003)
Tjaden, B., Goodwin, S.S., Opdyke, J.A., Guillier, M., Fu, D.X., Gottesman, S., Storz, G.: Target prediction for small, noncoding RNAs in bacteria. Nucleic Acids Res. 34, 2791–2802 (2006)
Hébrard, M., Kröger, C., Srikumar, S., Colgan, A., Händler, K., Hintons, J.: RNAs and the virulence of Salmonella enterica serovar Typhimurium. RNA Biol. 9(4), 437–445 (2012)
Venkova-Canova, T., Patek, M., Nesvera, J.: Control of rep gene expression in plasmid pGA1 from Corynebacterium glutamicum. J. Bacteriol. 185(8), 2402–2409 (2003)
Tjaden, T.: Biocomputational Identification of Bacterial Small RNAs and Their Target Binding Sites. In: Mallick, B., Ghosh, Z. (eds.) Regulatory RNAs: Basics, Methods and Applications. Springer (2012)
Gottesman, S.: The small RNA regulators of Escherichia coli: roles and mechanisms. Annu. Rev. Microbiol., 58303–58328 (2004)
Storz, G., Gottesman, S.: Versatile roles of small RNA regulators in bacteria. In: Gesteland, R.F., Cech, T.R., Atkins, J.F. (eds.) The RNA World, 3rd edn., pp. 567–594. Cold Spring Harbor Laboratory Press, Cold Spring Harbor (2006) (2006
Rivas, E., Eddy, S.: The greater part of sRNAs known in bacteria, have been identified in Escherichia coli, which are conserved in closely related bacteria. Bioinformatics 16(7), 583–605 (2000)
Amin, A.: A need for a “whole-istic functional genomics” approach in complex human diseases. Arthritis Res. Ther. 5, 76–79 (2003)
Neuman, E., Gay, R.E., Gay, S., Müller-Ladner, U.: Functional genomics of fibroblasts. Curr. Opin. Rheumatol. 16, 238–245 (2004)
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Corredor, M., Murillo, O. (2014). Identification of Small Non-coding RNAs in Bacterial Genome Annotation Using Databases and Computational Approaches. In: Castillo, L., Cristancho, M., Isaza, G., Pinzón, A., Rodríguez, J. (eds) Advances in Computational Biology. Advances in Intelligent Systems and Computing, vol 232. Springer, Cham. https://doi.org/10.1007/978-3-319-01568-2_42
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DOI: https://doi.org/10.1007/978-3-319-01568-2_42
Publisher Name: Springer, Cham
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