Question: Non-coding RNA prediction using genomic data
0
gravatar for nancydong20
3.3 years ago by
nancydong20100
nancydong20100 wrote:

Hello everyone!

I am trying to analyze non-coding RNAs in a newly assembled genome. I had tried Infernal (as reported in published studies), but our collaborator recommended to predict different types of non-coding RNAs (ex. miRNA, tRNA, rRNA) separately using more dedicated tools? For example, predict tRNAs using tRNAscan-SE (which I did and completed), predict miRNAs and rRNAs using BLAST with the respective databases.

I have tried to use BLAST with the miRBase, but I am getting very short alignments and I'm not sure how meaningful it is.

What is the best way to analyze non-coding RNAs in genomic sequence (which I know isn't going to be very accurate anyways)?

Thank you very much!

non-coding rna genome • 953 views
ADD COMMENTlink modified 3.3 years ago by cschu1812.3k • written 3.3 years ago by nancydong20100

As far as miRNAs go, you could use miRDeep2 in order to get microRNAs, but be advised, you will need small RNA-seq data to get it up and running.

ADD REPLYlink written 3.3 years ago by biofalconch460
0
gravatar for cschu181
3.3 years ago by
cschu1812.3k
cschu1812.3k wrote:

You could scan your genome one more time with Infernal http://eddylab.org/infernal/...

Edit: failed to see that OP already used this and now trying to get out of an embarrassing situation with humour. :P

ADD COMMENTlink modified 3.3 years ago • written 3.3 years ago by cschu1812.3k

Looks like OP has already done that.

ADD REPLYlink written 3.3 years ago by genomax85k

Blargh. I didn't see that.

ADD REPLYlink written 3.3 years ago by cschu1812.3k

No worries! I wonder why the collaborator recommended that I scan for them separately. Is it going to be more sensitive if I do it separately?

ADD REPLYlink written 3.3 years ago by nancydong20100
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 859 users visited in the last hour