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9 months ago
Ashok
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I have fasta format multiple RNA sequences (cajanus cajan). I have to separate the RNA sequences into coding and non coding sequences based on coding potential and length of open reading frame. Then again I have to separate the long non coding RNA and microRNA from the non coding RNA's. Similarly, I have to separate the microRNA from the coding RNA. Those above thing I have to do in R. Finally with this I have to develop one R package.
From fasta format rna sequences as input to filterout of lncra,mirna as output.
Please share your knowledge Your answers are welcome
It helps to be clear and open about the task at hand when you are asking for help. What kind of data do you have and what is the actual aim? You are asking about a tool but are not describing what kind of data you have on hand. Is this a new genome that you have put together and translated the reading frames from? Is it pro- eu-karyotic organism?
Sir,sorry for all.i am new to this.
Please tell code or packages related to this
Can you show us the science behind classifying RNA based on coding potential and ORF length? R packages implement algorithms that are based on logic which is based on scientific hypotheses/theories. Can you show us a paper that talks about this classification?
A quick search brought a few papers/packages:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7671399/
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6486542/
https://www.biorxiv.org/content/10.1101/620880v1.full
https://www.sciencedirect.com/science/article/pii/S2001037020304979