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Mireval: a web tool for simple microRNA prediction in genome sequences

W. Ritchie, F.-X. Theodule, D. Gautheret
2008 Bioinformatics  
We have developed an online tool called mirEval which can search sequences of up to 10 000 nt for novel microRNAs in multiple organisms. It is a comprehensive tool, easy to use and very informative.  ...  Availability: The mirEval web server is available at  ...  ACKNOWLEDGEMENTS Funding: This work was supported in part by INCa grant PL0079, 'microRNA, stem cells and cancer'. Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/btn137 pmid:18453555 fatcat:oh4galfybvg75ozzvarvzjcsya

miREval 2.0: a web tool for simple microRNA prediction in genome sequences

Dadi Gao, Robert Middleton, John E. J. Rasko, William Ritchie
2013 Computer applications in the biosciences : CABIOS  
Result: We have developed miREval 2.0, an online tool that can simultaneously search up to 100 sequences for novel microRNAs (miRNAs) in multiple organisms. miREval 2.0 uses multiple published in silico  ...  This tool can be used to discover miRNAs from DNA sequences or to validate candidates from sequencing data.  ...  ACKNOWLEDGEMENTS The authors thank their colleagues at the Gene and Stem Cell Therapy Lab of Centenary Institute for useful comments on Web site display. Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/btt545 pmid:24048357 pmcid:PMC5994938 fatcat:vc5tgplgdzezfobzzenubqdo3e

miR-BAG: Bagging Based Identification of MicroRNA Precursors

Ashwani Jha, Rohit Chauhan, Mrigaya Mehra, Heikham Russiachand Singh, Ravi Shankar, Ramin Homayouni
2012 PLoS ONE  
Discovering miRNA candidate regions across the genome has been a challenging problem. Most of the existing tools work reliably only for limited datasets.  ...  Here, we have presented a novel reliable approach, miR-BAG, developed to identify miRNA candidate regions in genomes by scanning sequences as well as by using next generation sequencing (NGS) data. miR-BAG  ...  Acknowledgments MM is thankful to CSIR for her JRFship, RC is thankful to CSIR-EMPOWER for his fellowship, AJ is thankful to DBT, India for his fellowship, HRS is thankful to CSIR for his fellowship.  ... 
doi:10.1371/journal.pone.0045782 pmid:23049860 pmcid:PMC3458082 fatcat:vancxjvnpbfdxgtvjagro4dbmq

Identification and expression analysis of a microRNA cluster derived from pre-ribosomal RNA in Papaver somniferum L. and Papaver bracteatum L

Farshad Davoodi Mastakani, Gabriel Pagheh, Sajad Rashidi Monfared, Masoud Shams-Bakhsh, Turgay Unver
2018 PLoS ONE  
Computational methods provide a useful tool for mining conserved miRNAs in diverse species, which leaning on the available sequences in the public databases [27].  ...  EST sequences have been analyzed for identification and prediction of miRNAs in Brassica napus L. [24], Glycine max L. [7], P. somniferum L. [22], Helianthus annuus L. [25].  ...  We also to thank of Tayebeh Kakeshpour and Masud Akbari Motlag for all of their help in the lab and helpful comments on the manuscript. Author Contributions  ... 
doi:10.1371/journal.pone.0199673 pmid:30067748 pmcid:PMC6070170 fatcat:lkt6tovg2zhavjyqhswv7qxhzy

An Ariadne's thread to the identification and annotation of noncoding RNAs in eukaryotes

G. Solda, I. V. Makunin, O. U. Sezerman, A. Corradin, G. Corti, A. Guffanti
2009 Briefings in Bioinformatics  
Computational methods for ncRNA research require different approaches from the ones normally used in the prediction of protein-coding genes.  ...  Indeed, primary sequence alone is often insufficient to infer ncRNA functionality, whereas secondary structure and local conservation of portions of the transcript could provide useful information for  ...  In addition, this method has been implemented in a user-friendly online tool called MirEval that enables researchers with limited bioinformatics skills to conduct a thorough analysis of an input sequence  ... 
doi:10.1093/bib/bbp022 pmid:19383843 fatcat:ham63whbwnfflkuvqjnwqnl6ay

Human Ribosomal RNA-Derived Resident MicroRNAs as the Transmitter of Information upon the Cytoplasmic Cancer Stress

Masaru Yoshikawa, Yoichi Robertus Fujii
2016 BioMed Research International  
As a result, seventeen RNA sequences identical with known miRNAs were detected in the human rRNA and termed as rRNA-hosted miRNA analogs (rmiRNAs).  ...  Meanwhile, microRNA (miRNA), an important regulator of gene expression, is derived from both coding and noncoding region of the genome and is implicated in various diseases.  ...  For instance, they used MirEval web tool for sequence analysis and their study probably may be based on the older version of rRNA sequence data.  ... 
doi:10.1155/2016/7562085 pmid:27517048 pmcid:PMC4969525 fatcat:xjtla2haavfztgxjkuro7rhmhy