Anyone knows about bioinformatics tool for checking interaction between viral miRNA and human mRNA?

More Mohammad Pirouzfar's questions See All

Which is suitable for use with Python? MySQL or SQL Server?

Which is suitable for use with Python? MySQL or SQL Server? What is your suggestion?

01 March 2021 3,422 3 View

Sample modeling in ABAQUS software and its relationship with the real world?

About crack modeling in ABAQUS: Mode I (pure-tensile cracking) and Mode II (pure-shear cracking), these assumptions may be accruing in theoretical approach (ABAQUS) not practical in Lab....

19 February 2021 6,156 1 View

absorption= 1-mag(S(FP1:1,FP1:1)S(FP1:1,FP1:1))-mag(S(FP2:1,FP1:1)S(FP2:1,FP1:1)) is it correct for absorption ?

hi everyone I am simulating a unit cell structure in HFSS using Flouquet port having two modes for absorption I have used this formula:- absorption=...

17 February 2021 9,178 2 View

An article on the Iranian state's civil liability in the COVID-19 matter needs supervision; Is anyone interested in collaborating?

Hello. An article on the Iranian state's civil liability in the COVID-19 issue has been written in collaboration with a friend and a comparative look at law and biology. The article is ready to be...

15 February 2021 2,906 2 View

Inter-rater / inter-coder reliability for thematic analysis?

In my research, I have used metaphorical elicitation tasks to investigate learners' conceptualization of speaking fluency. In the analysis phase, I used thematic analysis to make themes out of...

10 February 2021 4,719 11 View

How to define two different phases with different species?

Hello all, I am trying to model CO2 being dissolved in a bubble column filled with water. For mass transfer definitions, I need to define two phases: for instance, liquid and gas, where the liquid...

08 February 2021 2,722 3 View

What is the type or grade of ethanol used in SOL-GEL?

I'm preparing materials that will be use in SOL-GEL to produce silica gel, I will use Tetraethyl orthosilicate (TEOS) as precursor, and ethanol as solvent , but when I search to buy ethanol, the...

01 February 2021 5,153 4 View

Where to buy optically clear, low viscosity, refractive index 1.5-1.4 Silicone Oil ?

For research purposes, it is required to have optically clear, low viscosity silicone oil with a refractive index of 1.5-1.4. It is going to be used in optoelectronic research. Online purchase is...

01 February 2021 9,160 3 View

Can any one provide information about medicine, epidemic and critical issues or it is mandatory to be an expert ?

Due to the pandemic of coronavirus, the most source that the people depend on was social media. There is no guaranteed solution that is biased from political opinion. An example of that the...

01 February 2021 7,567 3 View

How can solve/disperse silicon nanoparticles in water?

I want to add silicon nanoparticles to my hydrogel, but when I sonicated these particles with water to disperse them in water, they agglomerated on the water's surface. How can I disperse them in...

26 January 2021 213 4 View

How to repeat an operation on an atom selection for multiple times in PyMol?

Hi, I am trying to construct a multi-layer fibril structure from a single layer in PyMol by translating the layer along the fibril axis. For now, I am able to use the Translate command in PyMol...

02 March 2021 4,569 4 View

How to calculate average trend in maximum annual NDVI from MODIS?

I am wanting to calculate the average trend in maximum annual NDVI in Iceland from 2010-2020 using MODIS MYD13Q1 V6. How would I do this? I have currently inserted the NDVI bands from the MODIS...

02 March 2021 752 2 View

Why does two different bioinformatics tools for the same proteins show different subcellular localizations?

During a computational analysis, I found that for a protein of a plant, two different subcellular localizations are seen using CELLO and WoLF PSORT. For example, in CELLO, it identified the...

01 March 2021 6,729 2 View

What is the most suitable server for predicting protein structures in bacteria?

I have used the i-Tasser several times, however it has been unavailable for several days. I tried the swiss-model, but the output was not very pleasant due to the model used. Is there any other...

28 February 2021 4,521 3 View

MiRNA qpcr problem?

Dear All, mirna primer showing some problem in the melting curve? any idea why? As attached is the melting curve. The forward sequence is obtained from miRBase and reverse primer is universal.

28 February 2021 5,008 4 View

What is the difference between genotype and haplotype data in the ped format?

Hi everybody In the ped format for genotype, alleles of any SNP are represented by two columns (one for each allele, separated by a space). Is a column sufficient for the haplotype to...

27 February 2021 1,965 1 View

Why is the efficiency of viral mRNA electroporation in PBMC low?

Hello, I have been struggling with the electroporation of PBMC with HIV-I mRNA. Although the quality of the RNA generated is good, and the handling of the cells in meticulous, the frequency of...

27 February 2021 9,233 3 View

I have need of XRD graph analysis software for phase identification. Can you please provide links for software tools which can be downloaded?

i am trying to download x'pert high score software, but can't download it. please do suggest software for phase analysis

24 February 2021 5,687 4 View

Can MicroRNA cross the blood brain barrier?

In diseased conditions, many genes and gene products are visible in the bloodstream. So my question is whether we can find traces of microRNA which is involved in disease and disorder in blood serum?

24 February 2021 7,064 3 View

Is it efficient to do liquid biopsy to investigate the gene expressions of the tumor?

To do liquid biopsy and look for specific gene expressions there are so many published papers. Thera are different protocols and procedures used to isolate circulating cell free RNA or mRNA from...

23 February 2021 7,326 5 View

Mohammad Alzeyadi

hi..

There are several online tools that you can use to predict the binding of a viral miRNA with the 3' UTR region of a human mRNA. Some examples include:

miRDB: This is a comprehensive database of miRNA target predictions and functional annotations. It allows you to search for target genes of a specific miRNA, and also provides information on the predicted binding sites and the strength of the interaction.

TargetScan: This is a widely used tool for predicting miRNA target sites. It uses a combination of conservation, thermodynamics, and mRNA structure to predict the likelihood of miRNA binding.

miRTar: This tool uses a machine learning approach to predict miRNA target sites. It allows you to search for target genes of a specific miRNA, and provides information on the predicted binding sites and the strength of the interaction.

I hope this information is helpful.

Saurabh Mandal

Check these papers, it looks like the authors have used many techniques to understand virus miRNA & their human mRNA target.

Article ViTa: Prediction of host microRNAs targets on viruses

Article In silico analysis of genomic landscape of SARS-CoV-2 and it...

Article Bioinformatics and systems biology approaches to identify mo...

Regards

Saurabh

Mohammad Pirouzfar

Thank you Mohammad Alzeyadi and Saurabh Mandal for your recommendations.

Susanta Roy

https://www.targetscan.org/vert_80/