MIREAP protocols

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MIREAP statistics

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MIREAP specifications

Information


Unique identifier OMICS_00376
Name MIREAP
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina, Life Technologies, Roche
Operating system Unix/Linux
Programming languages Perl
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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MIREAP in pipelines

 (9)
2018
PMCID: 5908857
PMID: 29674749
DOI: 10.1038/s41598-018-24477-x

[…] search against the mirna database, mirbase 19.0 (http://www.mirbase.org/). the reads, not being annotated to any known categories, were used to predict novel mirnas by the mirna prediction software mireap (http://sourceforge.net/projects/mireap/), by aligning with c. songorica transcriptome data (prjna356791). novel mirna precursors were also predicted using the same data set., the potential […]

2016
PMCID: 4884397
PMID: 27234464
DOI: 10.1186/s12870-016-0808-2

[…] mirnas of certain lengths and the base bias for each position of all identified mirnas, respectively. the novel mirna was de novo identified by mapping to the genome and predicting loci using mireap., to identify differences in mirnas expression levels under salt stress, the number of reads for each identified mirna was normalized against the total number of reads in the corresponding […]

2016
PMCID: 5036098
PMID: 27667199
DOI: 10.1038/srep32805

[…] tobacco est or gss sequences were used to identify novel mirnas by predicting precursors and their secondary structures using rnafold (http://www.tbi.univie.ac.at/rna/rnafold.1.html) and analyzed by mireap (http://sourceforge.net/projects/mireap/). all filtered small rnas that could fold into a stem-loop structure were considered to be mirnas., the frequency of mirnas was normalized […]

2016
PMCID: 5066493
PMID: 27619233
DOI: 10.1093/jxb/erw338

[…] fasta36 (http://faculty.virginia.edu/wrpearson/fasta/fasta36/), allowing three mismatches. the novel mirnas were identified from the unmatched reads. the putative mirna precursors were identified by mireap (https://sourceforge.net/projects/mireap/) according to the criteria of . only those with precursors found in the genome were identified as conserved or novel mirnas., the potential mirna […]

2015
PMCID: 5635596
PMID: 26527651
DOI: 10.1093/gbe/evv206

[…] reads that matched perfectly to less than 30 genomic regions in the b. rapa genome were used for mirna annotation. the mapped regions were subjected to secondary hairpin structure prediction using “mireap” (http://sourceforge.net/projects/mireap/, last accessed november 04, 2015). the predicted structures with less than −18 kcalmol−1 free energy, less than 300 nt spaces between the mirna […]


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MIREAP in publications

 (341)
PMCID: 5940789
PMID: 29739971
DOI: 10.1038/s41598-018-25103-6

[…] reads were searched against mirbase 21.0 to identify known mirnas in chicken and known mirnas in other species. based on their genome position and hairpin structures predicted by the software mireap_v0.2, novel mirna candidates were identified. the mirna expression level was calculated and normalized to transcripts per million (tpm). we identified mirnas with a fdr < 0.05 and fold […]

PMCID: 5923184
PMID: 29704894
DOI: 10.1186/s12917-018-1468-2

[…] the known chv-encoded mirnas including the pre-mirna sequences, length and count of reads would be obtained. the remaining srna reads mapped to genome were subjected for novel mirna prediction. mireap software (http://sourceforge.net/projects/mireap/) was used to predict novel mirna by exploring the secondary structure. dicer cleavage sites and predicted minimum free energies of unannotated […]

PMCID: 5932338
PMID: 29755439
DOI: 10.3389/fmicb.2018.00818

[…] fungi database using bowtie (). after removal of known non-coding rnas (rrna, trna, snrna, and snorna) by blast or bowtie, the unannotated small rnas were used for novel mirna prediction by using mireap (). the raw abundance of milrnas was normalized according to transcripts per million (tpm) normalization, where the n_base is 1,000,000 (; ). psrobot () and targetfinder () were used […]

PMCID: 5937831
PMID: 29690862
DOI: 10.1186/s12864-018-4678-x

[…] by exploring potential mirna precursor sequences with characteristic hairpin structures. there are many ways to predict novel mirnas, but no method is clearly superior []. in our study, we used the mireap software (http://sourceforge.net/projects/mireap/) which is suitable for plants to predict novel mirna by exploring the secondary structure, the dicer cleavage site and the minimum folding […]

PMCID: 5908857
PMID: 29674749
DOI: 10.1038/s41598-018-24477-x

[…] search against the mirna database, mirbase 19.0 (http://www.mirbase.org/). the reads, not being annotated to any known categories, were used to predict novel mirnas by the mirna prediction software mireap (http://sourceforge.net/projects/mireap/), by aligning with c. songorica transcriptome data (prjna356791). novel mirna precursors were also predicted using the same data set., the potential […]


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