Question: Could anyone please help me in identifying novel miRNAs from plant species without a reference genome?
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gravatar for anjalinair20
3.7 years ago by
India
anjalinair200 wrote:

 I am working on MicroRNA seq data analysis. I have completed the preprocessing steps and a blastn search was performed against plant mature MicroRNAs from miRBase to identify conserved miRNAs. It is mentioned in many reference papers that sequences are mapped to a reference genome for novel miRNA prediction. But the whole genome sequence or ESTs of my plant species is not reported. Could any one please help me regarding this?
 

rna-seq next-gen • 1.9k views
ADD COMMENTlink modified 3.6 years ago by Mohammad Reza Bakhtiarizadeh290 • written 3.7 years ago by anjalinair200
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gravatar for vassialk
3.7 years ago by
vassialk190
Belarus
vassialk190 wrote:

It is hardly possible do do any effective rational WGS research without an annotated already investigated reference files. Try to ask the authors of papers, perhaps, there are some known parts of the genome you need and you can compare yours with them. BW.

ADD COMMENTlink written 3.7 years ago by vassialk190
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gravatar for andrew.j.skelton73
3.7 years ago by
London
andrew.j.skelton735.7k wrote:

As hacky as this sounds, if you're looking at it from a purely investigative perspective you could do the following:

Download a closely related species from miRBase (hairpin and mature sequences) - This will be your reference, as miRNAs are generally pretty well conserved. 

Run miRDeep2 with the above as your reference, and grab some other closely related ones as it'll be required as a parameter. 

miRDeep2 is run on a per sample basis, not a whole experiment, so you're limited to your individual samples. 

ADD COMMENTlink written 3.7 years ago by andrew.j.skelton735.7k
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gravatar for Mohammad Reza Bakhtiarizadeh
3.6 years ago by
Tehran university

Hi

You can try these software:

MIRPIPE

miReader

MirPlex

ADD COMMENTlink written 3.6 years ago by Mohammad Reza Bakhtiarizadeh290
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