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miRNAminer specifications

Information


Unique identifier OMICS_00409
Name miRNAminer
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for miRNAminer

miRNAminer in publications

 (6)
PMCID: 4517789
PMID: 26218736
DOI: 10.1371/journal.pone.0134310

[…] genome (umd 3.1)., a computational method to find conservation across mammal species was used to aid verification of novel mirnas. this approach is somewhat similar to the one used by the authors of mirnaminer []. a custom python script using the pycogent [] library was written that utilises the ensembl compara programming interface. for each novel mirna, syntenic alignments from ensembl (39-way […]

PMCID: 3972105
PMID: 24690883
DOI: 10.1371/journal.pone.0093751

[…] . this includes the homologous mirs, related to each other by descent from a common ancestral dna sequence, that are either included in mirbase v.16 or were identified by a full cross-search using mirnaminer . for a total of 49 species, the conservation scores are available for more than 2,300 mirs within a range of 0 to 1. the 9 novel ir hubs and the 14 co-expressed mir hubs […]

PMCID: 3034697
PMID: 21247453
DOI: 10.1186/1471-2164-12-47

[…] these findings suggest that the yield of a homology-based analysis is very dependent on the available content of mirbase. artzi et al. used their recently released homology search web-server, mirnaminer, to increase the number of mirbase mirnas for seven mammals by 50%, identifying 790 new mirnas []. the strategy and filtering steps used by mirnaminer are very similar to those used […]

PMCID: 3089466
PMID: 21247879
DOI: 10.1093/nar/gkq1325

[…] rats (see mirbase: http://www.mirbase.org). the mir-351 gene is found only in mice and rats (a). additional mirna gene identifying algorithms could not locate mir-351 gene in any other animal (see mirnaminer: http://groups.csail.mit.edu/pag/mirnaminer and mirviewer: http://people.csail.mit.edu/artzi/mirviewer). mir-351 belongs to the mir-125 family, shown to perform varied roles […]

PMCID: 3026368
PMID: 20946604
DOI: 10.1186/1471-2105-11-S6-S20

[…] 15% of mirnas are expressed in clusters, and 25% are in introns []., if an rna is functionally significant, then the structure and sequence are conserved over the generations. a method called mirnaminer [] searches for such evolutionarily related mirna sequences from different species (homologs). given a query mirna, candidate homologs from different species are tested for secondary […]


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miRNAminer institution(s)
Massachusetts Institute of Technology, Cambridge, MA, USA

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