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Mireval: a web tool for simple microRNA prediction in genome sequences
2008
Bioinformatics
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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
2013
Computer applications in the biosciences : CABIOS
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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
2012
PLoS ONE
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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
2018
PLoS ONE
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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
2009
Briefings in Bioinformatics
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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
2016
BioMed Research International
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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