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MiRNAs are small-non-coding-RNA molecules with ~22 nt in length that control gene expression. IsomiRs are miRNA variants that vary in length and/or sequence when compared to their canonical forms and can display additions or deletions of one or more nucleotides at the 5' or 3' ends or both, internal editings or 3' end tailings. Consequently, isomiRs might regulate the expression of different targets in comparison to their respective canonical form, affecting the pathways of many known biological processes.

The IsomiR Window performs the integrated analysis of small-RNA-seq datasets with a user-friendly graphical interface, enabling the discovery of all types of miRNA variants through a Web application. Some of its features are:

1 Detection and quantification of animal or plant sncRNAs in two different experimental conditions, allowing for the processing of multiple datasets in simultaneous;

2 Identification of all possible types of isomiRs and prediction of their targets and consequent functional impact;

3 Generation of user-interactive plots and charts that can be customized and exported.

Instalation and usage

The IsomiR Window is deployed as a Virtual Machine. For full details about how to install and use the IsomiR Window VM please go http://isomir.fc.ul.pt/ to and read the IsomiRWindow_VM_instalation_manual.pdf.

Usage of the IsomiR Window pipeline

The scripts that process data and invoke different tools can be used in standalone version. Please see wiki pages:

https://github.com/andreiaamaral/IsomiR-Window/wiki/Annotation-module

https://github.com/andreiaamaral/IsomiR-Window/wiki/Functional-module

Contact

For IsomiR Window related questions please contact: andreiaamaral@fmv.ulisboa.pt

Funding

This project was co-funded by:

    FCT/UID/CVT/00276/2019

    FCT/UID/Multi/04046/2013

    FCT/UID/CEC/00408/2013