mirDBA specifications

Information


Unique identifier OMICS_14802
Name mirDBA
Interface Web user interface
Restrictions to use None
Input data A set of reads mapped to a genomic region of interest
Input format BED
Programming languages Perl, R
Computer skills Basic
Version 1.0
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Jan Gorodkin <>

Publication for mirDBA

mirDBA in publications

 (3)
PMCID: 5601128
PMID: 28947960
DOI: 10.18632/oncotarget.18557

[…] filtration (figure )., potential targeted genes of mirnas were predicted in databases of targetscan (http://www.targetscan.org/vert_71/), microrna.org (http://www.microrna.org/microrna/home.do) and mirdba (http://www.mirdb.org/mirdb/). networks analyses showed that 5 aberrantly expressed mirnas (mir-638, mir-5787, mir-8075, mir-6869-5p and mir-548c-5p) might be involved in the process […]

PMCID: 4437211
PMID: 26042150
DOI: 10.3389/fgene.2015.00188

[…] loops by secondary structure prediction method (rnafold) have been shown to form base-paired regions using experimental methods (zheng et al., ; li et al., )., the recently developed method, mirdba address these shortcomings by predicting mirnas purely based on the pattern by which the short reads map to a certain genomic region (read profile; figures , ) (pundhir and gorodkin, ). […]

PMCID: 4124155
PMID: 24917120
DOI: 10.1186/1471-2164-15-459

[…] support or experimental evidence these are not annotated with high confidence and are therefore only presented as a special track. for mirnas, the rna-seq profiles are particularly specific and the mirdba tool [] for aligning mirna rna-seq profiles directly against a compiled database of rna-seq profiles was developed in parallel with this work. future updates will use the full potential […]


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mirDBA institution(s)
Center for non-coding RNA in Technology and Health, Department of Veterinary Clinical and Animal Sciences (IKVH), University of Copenhagen, Frederiksberg C, Denmark
mirDBA funding source(s)
This work is funded in part by the Danish Strategic Research Council (Strategic Growth technologies), the Danish Independent Research Council (Technology and Production), and the Danish Center for Scientific Computation.

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