miREvo protocols

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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

 (12)
2018
PMCID: 5948824
PMID: 29751742
DOI: 10.1186/s12864-018-4736-4

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

2017
PMCID: 5377590
PMID: 28420964
DOI: 10.3389/fnmol.2017.00091

[…] were identified base on the data of lncrnas with find_circ (memczak et al., ). clean reads were screened the lengh of 21–22 nt as mirna, and located to reference sequence with bowtie. combined with mirevo software (wen et al., ) and mirdeep2 software (friedländer et al., ) to analysis the funtions of new mirnas. adopt deseq2 with negative binomial distribution (love et al., ) to analyse […]

2017
PMCID: 5507411
PMID: 28700597
DOI: 10.1371/journal.pone.0180085

[…] statistics of the mapped reading on silkworm chromosome was obtained and srnas were aligned with known mirnas using information on sequence, length, and secondary structure using mirbase. software mirevo: an integrative microrna evolutionary [] and mirdeep2 [] were integrated to predict novel mirnas through exploring the secondary structure (figs a-rr in ), the dicer cleavage site […]

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 []. 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 [, ]., the mirna expression levels were estimated by tpm (transcript per million) through the following criteria []: […]

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

[…] known mirnas, 338 mirnas overlapped in each group (). a total of 109 novel mirnas (79 from the cs group, 66 from the ts group, 59 from the ct group, and 69 from the tt group) were predicted through mirevo and mirdeep2 software (). fourteen were co-expressed in each group from novel mature mirnas. the read counts of these novel mirnas ranged from 1 to 1011., the number of differentially […]


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miREvo in publications

 (34)
PMCID: 5948824
PMID: 29751742
DOI: 10.1186/s12864-018-4736-4

[…] (http://www.mirbase.org), we used a modified version of mirdeep2 [] (https://www.mdc-berlin.de/8551903/en/) and srna-tools-cli (http://srna-tools.cmp.uea.ac.uk/) to predict secondary structures. mirevo [] and mirdeep2 [] were then used to predict novel mirnas by examining characteristics of the secondary structures, the dicer cleavage sites, and the minimum free energy of the folded models., […]

PMCID: 5941544
PMID: 29739311
DOI: 10.1186/s12864-018-4727-5

[…] the potential mirna and draw the secondary structures. in addition, srna precursors containing classic hairpin structure of mirna but not mapped to mirbase were used to predict novel mirnas. the mirevo and mirdeep2 were integrated to predict novel mirna through exploring the secondary structure, the dicer cleavage site and the minimum free energy of the small rna tags unannotated […]

PMCID: 5862966
PMID: 29563515
DOI: 10.1038/s41598-018-23334-1

[…] were found in b. napus, eight in b. rapa (mir5713, mir5714, mir5716, mir5724, mir9553, mir9556, mir9561 and mir9567) and none in b. oleracea.figure 3, furthermore, novel mirnas were discovered with mirevo and mirdeep 2 according to the hairpin structure of the mirna precursors, the dicer cleavage site and predicted free energy. a total of 69, 55 and 38 novel mirnas were identified in b. napus, […]

PMCID: 5788541
PMID: 29377917
DOI: 10.1371/journal.pone.0191564

[…] known mirnas were confirmed through mapping the reference mirbase20.0 using modified software of mirdeep2 [] and srna-tools-cli and custom scripts. novel mirnas were predicted by integrating the mirevo [] and mirdeep2 [] softwares. mature mirna expression levels were estimated by transcript per million (tpm) with the following equation []: normalized expression = mapped read-count / total […]

PMCID: 5723928
PMID: 29270184
DOI: 10.3389/fpls.2017.02081

[…] reference sequence in mirbase21.0 by bowtie (langmead et al., ), without mismatch to look for known mirnas. then, the other reads were integrated to predict novel mirnas using the available software mirevo (wen et al., ) and mirdeep2 (friedlander et al., ). the mirna counts as well as base bias were identified using custom scripts. the mifam.dat (http://www.mirbase.org/ftp.shtml) was used […]


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

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