Which tool to use to predict lncRNA-mRNA interaction?

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Martin Bartas

Hello, Mirjana Polovic,

did you try this user-friendly tool?

http://www.cuilab.cn/lnctar

There was no problem with lncRNA over 3 000 nt long.

Please, let me know, if it works or not.

Martin

Mirjana Polovic

Hello, Martin Bartas,

thank you for your answer.

I have tried this tool.

The message I get is the following:" The LncRNA and mRNA that you submitted are not predicted to interact with each other, suggest you adjust the ndG or try other pairs!"

Do you know how could I overcome this?

Best regards,

Mirjana

Shajahan Anver

What do you mean by interaction? If it is antissense then prediction programs should say it interacts since they are complementary. But, if you are looking for experimental evidence then it will be easier to check specific literature which reports this lncRNA. If it is not reported, then doing a strand specific quantitative RT-PCR for both mRNA and lncRNA first under conditions when this antisense ncRNA is upregulated/expressed will tell you whether there is any functional connection between these two RNAs. If they are anti correlated/ or some other cler interaction, then it will be interesting to further investigate experimentally whether they physically interact!

Hello, Shajahan Anver,

Thank you for your answer.

By interactions I mean on the first place on suppression of mRNA by lncRNA. I would like to find out if any predictions tools can do that. Experimental approaches are not an option at the moment.

Hello, Mirjana,

you may try to use less strict normalized deltaG parameter, default is -0.1. Try set up this parameter to zero value.

I have tried changing ndG to smaller and higher values but I always got the same message.

Hello,

then it probably means that no interactions were predicted by this tool. There is another tool, if you want to check previous results: http://rna.informatik.uni-freiburg.de/IntaRNA/Input.jsp, but your lncRNA must be smaller than 2000 nt, so you can cut your lncRNA sequence to 3 subsequences (first half, second half and the middle part) and submit separately.

Padmanaban Mohanan

Hi Mirjana and Martin

I tried this http://www.cuilab.cn/lnctar tool

I tried both ndG values to -0.5 & -0.1 and has got the same result in terms of interaction parameters