:: DESCRIPTION
miRNA Digger is a pipeline for large-scale identifiction of the new microRNA genes by screening the cleavage signals resided within the genome.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
miRNA Digger: a comprehensive pipeline for genome-wide novel miRNA mining.
Yu L, Shao C, Ye X, Meng Y, Zhou Y, Chen M.
Sci Rep. 2016 Jan 6;6:18901. doi: 10.1038/srep18901.
:: DESCRIPTION
GemiNI /dChip-GemiNi (Gene and miRNA Network-based Integration) is a web server which is an integrative analysis of gene and miRNA expression profiles with transcription factor-miRNA feed-forward loops
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Nucleic Acids Res. 2012 Sep 1;40(17):e135.
Integrative analysis of gene and miRNA expression profiles with transcription factor-miRNA feed-forward loops identifies regulators in human cancers.
Yan Z, Shah PK, Amin SB, Samur MK, Huang N, Wang X, Misra V, Ji H, Gabuzda D, Li C.
:: DESCRIPTION
mirConnX is a user-friendly web interface for inferring, displaying and parsing mRNA and microRNA (miRNA) gene regulatory networks. mirConnX combines sequence information, and computational predictions with gene expression data analysis to create a disease-specific, genome-wide regulatory network.
::DEVELOPER
SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
Nucleic Acids Res. 2011 Jul;39(Web Server issue):W416-23. doi: 10.1093/nar/gkr276. Epub 2011 May 10.
mirConnX: condition-specific mRNA-microRNA network integrator.
Huang GT, Athanassiou C, Benos PV.
:: DESCRIPTION
MIRPIPE enables rapid and simple browser-based miRNA homology detection and quantification.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
MIRPIPE – quantification of microRNAs in niche model organisms.
Kuenne C, Preussner J, Herzog M, Braun T, Looso M.
Bioinformatics. 2014 Aug 26. pii: btu573.
:: DESCRIPTION
CCmiR is a software for competitive and cooperative microRNA binding prediction
::DEVELOPER
Hu Lab – Data Integration and Knowledge Discovery @ UCF
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Bioinformatics. 2018 Jan 15;34(2):198-206. doi: 10.1093/bioinformatics/btx606.
CCmiR: a computational approach for competitive and cooperative microRNA binding prediction.
Ding J, Li X, Hu H.
:: DESCRIPTION
MITHrIL (Mirna enrIched paTHway Impact anaLysis) is an algorithm developed for the analysis of signaling pathways. It extends pathways by adding missing regulatory elements, such as microRNAs, and their interactions with genes.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Oncotarget. 2016 Aug 23;7(34):54572-54582. doi: 10.18632/oncotarget.9788.
Post-transcriptional knowledge in pathway analysis increases the accuracy of phenotypes classification.
Alaimo S, Giugno R, Acunzo M, Veneziano D, Ferro A, Pulvirenti A.
:: DESCRIPTION
SplamiR is the first method for the prediction of spliced miRNAs in plants. It takes genomic sequence and the sequence of a potential target mRNA as input. In the first phase of SplamiR, a database of complementary sequence pairs is created for the given genomic sequence. These sequence pairs might encode for RNAs folding into stem-loop structures. In the second phase, this database is searched for sequences with complementarity to the given target mRNA. For the identified sequences, in silico splice variants are generated and these are classified as to whether they might represent pre-miRNAs.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Bioinformatics. 2011 May 1;27(9):1215-23. doi: 10.1093/bioinformatics/btr132. Epub 2011 Mar 17.
SplamiR–prediction of spliced miRNAs in plants.
Thieme CJ, Gramzow L, Lobbes D, Theissen G.
:: DESCRIPTION
miFRame which supports the analysis of human small RNA NGS data is a web server for analysis and visualization of miRNA sequencing data in neurological disorders.
::DEVELOPER
Chair for clinical bioinformatics
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation:
J Transl Med. 2015 Jul 14;13:224. doi: 10.1186/s12967-015-0594-x.
miFRame: analysis and visualization of miRNA sequencing data in neurological disorders.
Backes C, Haas J, Leidinger P, Frese K, Großmann T, Ruprecht K, Meder B, Meese E, Keller A
:: DESCRIPTION
MiRCat is a revolutionary new way of sharing and analysing sequencing data for small RNA.
::DEVELOPER
Victor Chang Cardiac Research Institute
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Nucleic Acids Res. 2013 Aug 1;41(15):e147. doi: 10.1093/nar/gkt485. Epub 2013 Jun 17.
miRspring: a compact standalone research tool for analyzing miRNA-seq data.
Humphreys DT, Suter CM.
:: DESCRIPTION
MIRcheck is a perl script designed to identify RNA sequences with secondary structures similar to plant miRNAs. It compares a potential miRNA and precursor against a set of secondary structure constraints derived from known plant miRNA precursors. The potential miRNA and precursor “pass” MIRcheck if all requirements are met, and “fail” MIRcheck if one or more is not.
::DEVELOPER
Bartel Lab at Whitehead Institute for Biomedical Research
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Mol Cell. 2004 Jun 18;14(6):787-99.
Computational identification of plant microRNAs and their targets, including a stress-induced miRNA.
Jones-Rhoades MW, Bartel DP.
