Question: Can anyone tell me the clear procedure for new or novel miRNA identification in animal??
Hi!
Currently i am working in miRNA identification based on EST of particular animal.. i did blastn search against the EST to identify the homologous of mature miRNA.. Next step is blastx to remove the protein coding sequences. How can i select the non-coding transcripts or EST's from those results? On what criteria i have to select?? Then I want to know how to select the range of precursors and mature miRNA? Based on secondary structure means how they find the mature miRNA? I read many articles but i am still not clear how to find those.. If anyone know plz help me..
Thanks,
Nandhini
Answers
0
Hi Nandhini,
I work in plant genomics and know few steps to identify miRNA in it. Following image from http://www.sciencedirect.com/science/article/pii/S1319562X13000442 summarizes the procedure for predicting potential miRNAs from coffee. I hope, it will be useful for miRNA identification in animal as well.
Thanks for your steps..I am having this procedure too but there are some to doubts to clarify. when we did blastn, we have to select 200nt up and down from the blast hits for precursors na.. then these ~400nt is loaded as input for blastx against the NR protein db.. Here how can we select the non-coding EST's from the blastx result? On what criteria?? Then my major doubt is when we do mfold, how can we select the best one? Still now i cant understand the concept for selecting the mature and precursor miRNA.. In all articles they gave based on these following criteria like this and mentioned 5-6 rules..From the secondary structure how can we know where the precursors and the mature miRNA? Can you explain this??
Hi Nandhini,
I work in plant genomics and know few steps to identify miRNA in it. Following image from http://www.sciencedirect.com/science/article/pii/S1319562X13000442 summarizes the procedure for predicting potential miRNAs from coffee. I hope, it will be useful for miRNA identification in animal as well.
Anyway, I will suggest you to please have a look at these tools http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2677885/
Best
Hi!
Thanks for your steps..I am having this procedure too but there are some to doubts to clarify. when we did blastn, we have to select 200nt up and down from the blast hits for precursors na.. then these ~400nt is loaded as input for blastx against the NR protein db.. Here how can we select the non-coding EST's from the blastx result? On what criteria?? Then my major doubt is when we do mfold, how can we select the best one? Still now i cant understand the concept for selecting the mature and precursor miRNA.. In all articles they gave based on these following criteria like this and mentioned 5-6 rules..From the secondary structure how can we know where the precursors and the mature miRNA? Can you explain this??
Thanks,
Nandhini
— Nandhini devi 3759 days ago
My doubt is how to fix the range of precursors? like from x to y nucleotide..
— Nandhini devi 3758 days ago