Software - RNAmicro

If you find RNAmicro useful, please cite the following publication:
J Hertel and P F Stadler.
Hairpins in a Haystack: recognizing microRNA precursors in comparative genomics data. Bioinformatics, 22(14):e197-202, 2006.
RNAmicro is a machine learning tool, with the purpose to distinguish miRNA precursor sequences from other (putative) non-coding RNAs.
Based on multiple sequence alignments a support vector machine, trained with all known metazoan miRNA precursor alignments and other non-coding RNAs, returns the probability how likely the input may be a miRNA precursor.
The webservice will be available again soon.
Requirements
Download
RNAmicro1.1.3 - latest release (September 2008)
RNAmicro1.0   - release according to publication on the top
Installation
Download the latest release of RNAmicro to a directory of your choice, say DIR-X.
Change into this directory:
$ cd DIR-X
Extract the files from the downloaded archive:
$ tar zxvf RNAmicro1.x.y.tgz
Note: You may have to edit the Makefile according to your installation of the Vienna RNA package and PCRE library.
Run the installation script:
$ ./install.sh
ERRORS may occur if you don't have all the required tools installed.
Whats new in RNAmicro1.1.1 ?
The initially published version of RNAmicro was composed by a structure filter followed by the extraction of 13 features which were taken as values of the description vector for a support vector machine.
In general, this is the same in version 1.0. However, a subset of features was replaced by different ones.
The modified version of RNAmicro has been applied to the same screens as the original one and the results have been compared.
Although, the total number of positive classified alignments is twice as many as in the older version, the statistical values improved significantly.
For details on the exact number see RNAmicro1.1.documentation.pdf