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PeerJ
2015 ; 3
(?): e1332
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miRMOD: a tool for identification and analysis of 5 and 3 miRNA modifications
in Next Generation Sequencing small RNA data
#MMPMID26623179
Kaushik A
; Saraf S
; Mukherjee SK
; Gupta D
PeerJ
2015[]; 3
(?): e1332
PMID26623179
show ga
In the past decade, the microRNAs (miRNAs) have emerged to be important
regulators of gene expression across various species. Several studies have
confirmed different types of post-transcriptional modifications at terminal ends
of miRNAs. The reports indicate that miRNA modifications are conserved and
functionally significant as it may affect miRNA stability and ability to bind
mRNA targets, hence affecting target gene repression. Next Generation Sequencing
(NGS) of the small RNA (sRNA) provides an efficient and reliable method to
explore miRNA modifications. The need for dedicated software, especially for
users with little knowledge of computers, to determine and analyze miRNA
modifications in sRNA NGS data, motivated us to develop miRMOD. miRMOD is a
user-friendly, Microsoft Windows and Graphical User Interface (GUI) based tool
for identification and analysis of 5' and 3' miRNA modifications (non-templated
nucleotide additions and trimming) in sRNA NGS data. In addition to
identification of miRNA modifications, the tool also predicts and compares the
targets of query and modified miRNAs. In order to compare binding affinities for
the same target, miRMOD utilizes minimum free energies of the miRNA:target and
modified-miRNA:target interactions. Comparisons of the binding energies may guide
experimental exploration of miRNA post-transcriptional modifications. The tool is
available as a stand-alone package to overcome large data transfer problems
commonly faced in web-based high-throughput (HT) sequencing data analysis tools.
miRMOD package is freely available at http://bioinfo.icgeb.res.in/miRMOD.
free
free
free
