miR-PREFeR statistics

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miR-PREFeR specifications

Information


Unique identifier OMICS_04637
Name miR-PREFeR
Alternative name miRNA PREdiction From small RNA-Seq data
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for miRNA PREdiction From small RNA-Seq data

miR-PREFeR in pipeline

2017
PMCID: 5590963
PMID: 28886174
DOI: 10.1371/journal.pone.0184528

[…] other sequence was kept as a single end sequence and used in further analysis. the level of perfect duplicates was assessed with the aid of the python script process-reads-fasta.py, as part of the mir-prefer pipeline []. de-novo assembly of trimmed sequences was performed using the ‘de-novo assembly’ module of the clc, using the following parameters: bubble size 50, word size 24 and minimum […]


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miR-PREFeR in publications

 (7)
PMCID: 5590963
PMID: 28886174
DOI: 10.1371/journal.pone.0184528

[…] other sequence was kept as a single end sequence and used in further analysis. the level of perfect duplicates was assessed with the aid of the python script process-reads-fasta.py, as part of the mir-prefer pipeline []. de-novo assembly of trimmed sequences was performed using the ‘de-novo assembly’ module of the clc, using the following parameters: bubble size 50, word size 24 and minimum […]

PMCID: 5496985
PMID: 28698797
DOI: 10.1038/hortres.2017.31

[…] on bioinformatics tools, such as tophat, cufflinks, circexplorer, ciri, cpc and hmmer, for the discovery of ncrnas. recently, some new computational tools, for example, mirdeep-p, mirdeepfinder and mir-prefer were developed for the identification of plant mirnas, which are often belong to large families with high-sequence similarity among the paralogous members. moreover, these tools […]

PMCID: 5485680
PMID: 28651543
DOI: 10.1186/s12864-017-3869-1

[…] were detected to be specifically expressed in m82 and il9–1, respectively (fig. , additional file : table s1).fig. 5 , to identify putative novel mirnas in tomato, novel mirnas were predicted using mir-prefer. a total of 179 novel mirnas were predicted, among them, 46 were detected in all the four small rna libraries (fig. , additional file : table s2). different numbers of novel mirnas […]

PMCID: 5471329
PMID: 28663752
DOI: 10.3389/fpls.2017.00969

[…] criteria were used to filter out possible messenger rna (mrna) residues., to predict mirnas from small rna-seq data, using expression patterns and following the criteria for plant mirna annotation, mir-prefer () was used due to its low false-positive rate and running time. the mappable reads were aligned to the g. arboreum reference genome using bowtie2 () with zero mismatch and end to end read […]

PMCID: 5258749
PMID: 28174574
DOI: 10.3389/fpls.2016.02058

[…] together with their sequential isoforms, isomirs (bartel, ; wang et al., ; budak et al., ; budak and kantar, )., there are several tools for in silico mirna identification such as miranalyzer, mir-prefer, mirtrap, mirlocator, and mirena (hendrix et al., ; mathelier and carbone, ; hackenberg et al., ; lei and sun, ; cui et al., ). majority of these methods rely on the sequence information […]


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miR-PREFeR institution(s)
Department of Computer Science and Engineering, Michigan State University, East Lansing, MI, USA

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