DMISO

Author: Amlan Talukder\ Date: August 1, 2021

DMISO is a software used to predict interaction between the provided miRNA and target sequences. It was also trained to predict interaction between isomiR and their target sequences. It was developed by the computational System biology group at University of Central Florida.

INSTALLATION

Install Python 3.7 or higher

Create a virtual environment (optional but preferred)

    cd DMISO
    python -m venv ./.venv
    source ./.venv/bin/activate

Run the following to install necessary python packages
```
    make all
```

EXECUTION

You can run the software by running the script "dmiso.py" with the following command:

usage: dmiso.py [-h] -p PAIR -m MIRNA/ISOMIR -t MRNA [-o OUTPUT]

Predicts interactions between miRNA and target pair. It takes an input file of
query miRNA/isomiR and target pairs and predict the interactions between the
pairs. Alternatively, it can take separate files for miRNA/isomiR and target
sequences and outputs all the possible interactions.

optional arguments:
  -h, --help       show this help message and exit
  -o OUTPUT        Path for DMISO outputs

required arguments:
  -p PAIR          Path for miRNA (or isomiR) and mRNA pair file in a tsv
               format. The file must contain data in the following order:
               miRNA id, target id, miRNA sequence, target sequence
  -m MIRNA/ISOMIR  Path for miRNA or isomiR sequence in fasta format.
  -t MRNA          Path for mRNA sequence in fasta format.

Example: "python3 dmiso.py -p examples/test_pairs.txt -o examples/test_output.txt" OR
    "python3 dmiso.py -m examples/test_miRNAs.fa -t examples/test_mRNAs.fa -o examples/test_output.txt"

REQUIRED INPUTS

The tool takes a file path as mandatory parameter. The file must contain miRNA id, target id, miRNA sequence and target sequence in the tab delimited format. Alternatively, it can take separate files for miRNA/isomiR and target sequences and outputs all the possible interactions.

MODEL

The model file is stored under "models" directory.

RESULTS

The result file contains the miRNA and target information provided in the input file followed by a prediction score and prediction value.

miRNA ID    Target ID   miRNA Sequence  Target Sequence Prediction Score    Prediction
hsa-miR-7111-3p|MIMAT0028120    ENST00000569083.1_3|ENSG00000134419.15_7|RPS15A|protein_coding  UCCUCUUCUCCCUCCUCCCAG   CUUAAUUAAAAGAAGUUAAUGCUAAGAAUUUCUGUGGUGCAGUUUGACUUAAG   0.073714145 0
hsa-miR-4286|MIMAT0016916   ENST00000338086.9_5|ENSG00000055917.16_9|PUM2|protein_coding    ACCCCACUCCUGGUACCA  GUAGAUUAUUGGAAGAUUUCAGAAACAACCGCUUCCCAAACCUUCAGCUUAGA   0.07340459  0
hsa-miR-27a-3p|MIMAT0000084 ENST00000369158.1_2|ENSG00000203811.1_4|H3C14|protein_coding    UUCACAGUGGCUAAGUUCUUCU  CGGCAAGGCCCCGAGGAAGCAGCUGGCCACCAAGGCGGCCCGCAAGAGCGCGCCGG    0.99942267  1
hsa-miR-8089|MIMAT0031016   ENST00000264658.11_7|ENSG00000108306.13_13|FBXL20|protein_coding    UGAGGUCAGGGGAUUGGGAUUC  GGCUCACGCCUGUAAUCCCAGCACUUUGGGAGGCCGAGGCGGGCGGAUCACAAAGUGUCAGGAGUUUGAGAACAG 0.9987809   1

LICENSE & CREDITS

The software is freely available for academic use. plase contact Xiaoman (Shawn) Li (xiaoman@mail.ucf.edu) for further information.

CONTACT INFO

If you are encountering any problem regarding to DMISO, please refer the manual first. If problem still can not be solved, please feel free to contact us:\ Amlan Talukder (amlanaccount@gmail.com)\ Haiyan (Nancy) Hu (haihu@cs.ucf.edu)\ Xiaoman (Shawn) Li (xiaoman@mail.ucf.edu)

amlantalukder / DMISO

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