miREvo protocols

miREvo specifications

Information


Unique identifier OMICS_00406
Name miREvo
Software type Pipeline/Workflow
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl, Shell (Bash)
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.2
Stability Stable
Requirements RNAfold, Bowtie, BioPerl, mafsInRegion, BLAT
Maintained Yes

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Documentation


Maintainer


  • person_outline Ming Wen <>

Publication for miREvo

miREvo IN pipelines

 (5)
2018
PMCID: 5948824
PMID: 29751742
DOI: 10.1186/s12864-018-4736-4

[…] using bowtie [20] with no mismatches permitted, and the locations were used to identify known mirnas. novel mirnas were predicted using the applications mirevo [21] and mirdeep2 [22]. two hundred and thirty two unique mirnas including 141 conserved mirnas and 91 novel mirnas were identified and assigned to genomic coordinates (additional file 1: […]

2017
PMCID: 5617439
PMID: 28977879
DOI: 10.18632/oncotarget.18470

[…] contaminated reads. then, clean reads of 18-35 nt srna were mapped to a reference sequence by bowtie [40]. mapped srna tags were used to look for known mirna, and mirbase20.0 was used for reference. mirevo and mirdeep2 software were integrated to predict novel mirna targets [41, 42]., the mirna expression levels were estimated by tpm (transcript per million) through the following criteria [43]: […]

2017
PMCID: 5632538
PMID: 29018616
DOI: 10.7717/peerj.3881

[…] to reference sequence (amel_4.5) applying bowtie (langmead et al., 2009). mapped reads were used to identify known mirnas using mirbase 20.0 (griffiths-jones, 2010). novel mirnas were predicted with mirevo (ming et al., 2012) and mirdeep2 (friedländer et al., 2012) through exploring the characteristic hairpin structure, dicer cleavage sites and minimum free energy., all the sequencing data […]

2017
PMCID: 5637055
PMID: 29020916
DOI: 10.1186/s12864-017-4145-0

[…] were identified (additional file 4), which represented 10.86% of the total reads and 0.22% of the unique clean reads. additionally, 130 novel mature mirnas and 139 mirna precursors were found using mirevo [43] and mirdeep2 (additional file 5)., the mrna and lncrna expression levels were analyzed using cuffdiff v2.1.1 [36]. the overall expression levels of both lincrnas and antisense-lncrna […]

2016
PMCID: 5495669
PMID: 27660025
DOI: 10.5713/ajas.16.0325

[…] clean reads were mapped duck genome database (bgi duck 1.0 reference annotation release 101) and compared with the distribution of the known mirnas. the novel mirnas were predicted by the software mirevo and mirdeep2 [17,18]. with the statistics and normalization of the expression of mirnas in two samples through transcript per million (tpm, normalization expression = […]

miREvo institution(s)
State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China

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