Development of a New Pipeline for Identification and Characterization of Micro RNAs from Plants
Open source microRNA analysis pipelines for next generation sequencing data (NGS) often make necessary use and working knowledge of command line interface, massive data processing resources and expertise which is a daunting task for biologists. Further, the microRNA data generated from NGS platforms will not be in a form from which one could understand or make use of it. Hence a comprehensive pipeline has been developed by integrating several open source NGS tools along with a graphical user interface called sRNAbench. It is used for expression profiling of small RNAs and prediction of microRNAs from NGS data. The pipeline features functionalities such as read processing, sequence identification, target prediction and enrichment analysis. It provides even prediction of novel microRNAs and its sequences. The pipeline will be very useful for plant genomics community and it does not require knowledge in computational biology in order to discover miRNAs and utilize the same in genomics studies.
Victor M., MicroRNAs in differentiating tissues of Populus and Eucalyptus trees, 2006, Dissertation - University of Pretoria. http://repository.up.ac.za/handle/2263/26140
Lau NC, Lim LP, Weinstein EG, Bartel DP., An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans, Science, 2001; 294(5543):858-62.
Adai A., Johnson C, Mlotshwa S, Archer-Evans S, Manocha V, Vance V, et al.,. Computational prediction of miRNAs in Arabidopsis thaliana, 2005; Genome research 15:78-91
Zhao Y, Srivastava D.,A developmental view of microRNA function, Trends in Biochemical Sciences, 2007; 32:189-197.
Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ., miRBase: tools for microRNA genomics, Nucleic Acids Research, 2008; 36(Database issue): D154-8.
Hackenberg M, Sturm M, Langenberger D, Falcón-Pérez JM, Aransay AM., miRanalyzer: a microRNA detection and analysis tool for next-generation sequencing experiments, Nucleic Acids Research, 2009; 37(Web Server issue):W68-76. doi: 10.1093/nar/gkp347
Hackenberg M, Rodríguez-Ezpeleta N, Aransay AM., miRanalyzer: an update on the detection and analysis of microRNAs in high-throughput sequencing experiments, Nucleic Acids Research, 2011; 39(Web Server issue):W132-8. doi: 10.1093/nar/gkr247
Qian K, Auvinen E, Greco D, Auvinen P., miRSeqNovel: an R based workflow for analyzing miRNA sequencing data, Mol Cell Probes, 2012; 26(5):208-11. doi: 10.1016/j.mcp.2012.05.002.
Bertolini E, Verelst W, Horner DS, Gianfranceschi L, Piccolo V, Inzé D, et al., Addressing the Role of microRNAs in Reprogramming Leaf Growth during Drought Stress in Brachypodium distachyon, Molecular Plant, 2013; 6(2): 423–443. doi:10.1093/mp/sss160