miRMOD is the first windows based standalone GUI tool to identify and analyze non templated nucleotide additions and trimming
at both the termini of the miRNA sequences in NGS data. It provides useful statistics like kinds of miRNA modifications and
its frequencies, differential miRNA-modified miRNA abundance and frequencies of the modified bases found in each of the
modifications. miRMOD also analyzes differences in miRNA target interactions. This kind of detailed analysis helps understand
global as well as micro level miRNA modifications in NGS datasets. miRMOD provides user-friendly graphical representations
to visualize miRNA modifications and target predictions in different formats to facilitate HT data analysis even on your laptop .
miRMOD is also available in command line version to reach broad range of users.

Applications :
  1. Predicts modified miRNAs (5' and/or 3' non-templated nucleotide additions and trimming) .
  2. Percentage of occurence of each modified sequence in the dataset.
  3. Any miRNA to miRNA conversion as a result of trimming.
  4. miRNA score table to present its relative tendency to get modified.
  5. Determination of target binding alteration due to modification using RNAhybrid.
  6. Determine novel targets for modified miRNAs.

  Required input files:
  1. Mature miRNA(s) sequences (fasta format) for which modifcation(s) has to be identified.
  2. Small RNA sequencing reads processed using "Prepare_input" program (packaged with miRMOD).
  3. Bowtie alignment file generated using file prepared in 2. and reference genome/pre-miRNAs.
  4. Target sequence file (fasta format,optional).

  New Features (version 0.3):
  1. Results can be saved as session file (.mod).
  2. cross-platform command line version is now included in miRMOD package.
  3. miRNA score table to present its relative tendency to get modified.
 

Supplementary data (directory : sample) is included in miRMOD package or it can be downloaded from here

Complete manual with screen-shots can be downloaded from here

Freqenly asked questions:

ICGEB

miRNAs are a class of small ncRNA, found both in plants as well as animals, whose size ranges from 20 -24 nucleotides
acting as a posttranscriptional regulators of gene expression in a wide range of organisms. In animals, miRNA sequences
bind to complementary sequences often found in UTR regions of target mRNAs and induce translational repression of the
mRNA while in case of plants they bind either at the UTR regions or coding regions, causing mostly cleavage of the target
mRNAs.
miRNAs get modified subsequent to its biogenesis at 3' and 5' ends by various enzymes which plays an important
role in the stability of the miRNA. miRNAs are modified either by trimming, addition or substitution of nucleotides. Although
the role of modified miRNAs are yet to be established but these modifcation could affect the target binding abilities of miRNAs.