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miReader specifications


Unique identifier OMICS_11466
Name miReader
Software type Application/Script
Interface Command line interface, Graphical user interface
Restrictions to use None
Input data FASTQ or FASTA
Operating system Unix/Linux, Windows
Programming languages Java
Computer skills Advanced
Stability Stable
Maintained Yes


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  • person_outline Ravi Shankar <>

Publication for miReader

miReader in publications

PMCID: 5065965
PMID: 27800484
DOI: 10.3389/fvets.2016.00086

[…] mirnas in other species. this strategy has also been applied to the chinese hamster (). there are several computational resources for the identification of mirnas and their targets (). among these, mireader is a newly launched bioinformatics tool for the discovery of novel mirnas that can be used to identify mirnas that are not annotated in mirbase, yet without the need for reference genomic […]

PMCID: 4884428
PMID: 27233515
DOI: 10.1186/s12859-016-1036-3

[…] noradesk [] was the first method to incorporate structural energy based features and read coverage information to increase the detection accuracy of small ncrnas, including mirnas, whereas mireader [] relies only on hybridization patterns of the reads to detect mirnas., the hairpin analysis has been performed mostly through machine learning based predictive models. to obtain […]

PMCID: 4705652
PMID: 26578605
DOI: 10.1093/nar/gkv1221

[…] several tools have been devised to predict mirnas from ngs data. the most common are mirdeep/mirdeep2 (,) and miranalyzer (,). both can find previously known and novel mirnas. another recent tool, mireader (), identifies mature mirnas directly from ngs read data without the need for genomic sequences or homologous references. experimental techniques such as molecular cloning, sequencing […]

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miReader institution(s)
Studio of Computational Biology & Bioinformatics, Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
miReader funding source(s)
The present work was supported by ICAR grant NFBSFARA/RNA-3022/2012-13 and CSIR 12th FYP project GENESIS BSC0121.

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