Software

SplamiR - Predicting miRNAs in plants

Description

MicroRNAs regulate many biological processes in plants and animals. Recent sequencing efforts led to the discovery of miRNA genes containing introns, which could not be predicted directly from genomic sequence so far.

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.

Requirements

1. Linux operating system
2. Oracle/SUN Java SE Runtime Environment (tested on build 1.6.0+)
3. Internet connection for using the miR-abela classifier

Installation

SplamiR is precompiled for a Linux platform and does not need to be installed.

Please refer to the README-file provided in the downloadable zip-archive for further information.

Please note:

SplamiR is unfortunately not able to process multiple FASTA files. As a workaround, you can split your multiple FASTA file into single FASTA files using the following command:

csplit -z myfile.fas '/>/' '{*}'

You can then run SplamiR separately on the resulting files. We apologize for the inconvenience and will work on fixing the problem.