Computational identification of long non-coding RNA(lncRNAs) in plants

Question

[tinkugoutam]

how to identify long non-coding RNAs in plants by using In-Silico approaches.

Answer 1

[Antonio R. Franco]

There are some recent papers you can find that follow a pipeline to discover the lncRNA

Basically they BlastX all sequences and discard those with significant homology (because they are coding)

They discard everything is shorter than 200bp (miRNA, etc)

Then, they run a search with services like Coding Potential Calculator

Answer 2

[francescomusacchia]

My research group recently published this paper reporting a tool for detecting putative long non-coding RNAs. It uses both the heuristics which Antonio said.

Find the tool at: https://github.com/frankMusacchia/Annocript

The paper: http://bioinformatics.oxfordjournals.org/content/early/2015/02/19/bioinformatics.btv106

Find out the output it gives at: https://github.com/frankMusacchia/Annocript/blob/master/GUIDE/OUTPUT.md

Cheers

[saj98]

Hello Francesco

I am using Annocript to analyse my data, I am looking for lncRNA. I am new in bioinformatic, do have demo or short record showing how to use Annocript. I am in Rutgers University and I am trying to use this software with other students but it is a little complicated and needs a lot of expertise.

Thanks
Shaima

[Sanchita Gupta]

Hello tinkugoutam

Currently, I am also working on the in silico identification of long non coding RNAs in plants. We have made an in house bioinformatics pipeline for the identification of plant lncRNAs. You can share us your plant data with us for the analysis.

Thanks

Sanchita

[tinkugoutam]

Hello sanchita, Yes I am looking for the identification of lncRNA from my transcriptome data of wheat. How should you r going to help.

[Sanchita Gupta]

Hello tinkugoutam

For this you have to share transcriptome data of your plant.

[tinkugoutam]

I want to do it with my self. So if u please share your pipeline with me.

[Sanchita Gupta]

I will share only once it will get published.

Sanchita