Question: Identified Potential Non-Coding Rna, And Then?
12
gravatar for Michael Dondrup
10.0 years ago by
Bergen, Norway
Michael Dondrup47k wrote:

Assume we identify - by RNA-seq, tiling arrays, by prediction - possible candidate regions for non-coding, small RNAs. I wish to verify and predict the function of as many RNAs as possible by computation before going to the lab. One could use eg. Rfam to find similar sequences, after that we are left with more than 90% that have no match. One could predict the 2D structure using eg. RNAfold, compare that using RNAforester. But that does not get me even close to a function prediction. Do you have experience with other tools or a better computational pipeline that gets more information out of the ncRNA candidates, possibly even something specific to bacteria.

rna prediction sequence • 4.8k views
ADD COMMENTlink modified 22 months ago by RamRS27k • written 10.0 years ago by Michael Dondrup47k
1

could you share the identifying part for ncRNA using RNA-Seq?

ADD REPLYlink written 10.0 years ago by Bioinfosm620
1

Just searched regions with high coverage not overlapping with coding sequences. As here

ADD REPLYlink modified 9 months ago by RamRS27k • written 10.0 years ago by Michael Dondrup47k

And then? Experimental verification :-)

ADD REPLYlink written 10.0 years ago by Neilfws48k

@neil: so true ;) and of course, you cannot discover something that's not already annotated by a db search. unfortunately, my pipetting skills are rather underdeveloped.

ADD REPLYlink written 10.0 years ago by Michael Dondrup47k
12
gravatar for Fred Fleche
10.0 years ago by
Fred Fleche4.3k
Paris, France
Fred Fleche4.3k wrote:

[?]

http://www.bioinformatics.fr/resources.php?tag=non-coding-rnas

ADD COMMENTlink modified 4.3 years ago by Michael Dondrup47k • written 10.0 years ago by Fred Fleche4.3k
2

Great resource. After the site redesign, it looks like the link has changed to this.

ADD REPLYlink modified 22 months ago by RamRS27k • written 9.6 years ago by Brad Chapman9.5k
1

This is a good approach to start with. We did similar thing before heading to wet lab.

ADD REPLYlink written 10.0 years ago by Jaydon40

that's a good resource i hadn't heard of!

ADD REPLYlink written 10.0 years ago by brentp23k

The design is ugly but I am working on it (should be available in one or two months). Most of the ressources are from the NAR issues related to databases and webservers but organized by topics.

ADD REPLYlink written 10.0 years ago by Fred Fleche4.3k

Great resource, thank you. I will try with my data.

ADD REPLYlink written 10.0 years ago by Michael Dondrup47k

Thanks for the remark I did update my response with the new link

ADD REPLYlink written 9.6 years ago by Fred Fleche4.3k
6
gravatar for Paul Gardner
10.0 years ago by
Paul Gardner190
Christchurch, New Zealand.
Paul Gardner190 wrote:

How are you doing your comparison to Rfam? If you're just running rfam_scan.pl or the CMs then this may not give you the results you really want. See the recent paper by Kolbe & Eddy to hear more about the limitations of CMs on truncated sequences. Could explain some of your lack of sensitivity vs Rfam. However there is a terrifying number of ncRNAs not yet covered by Rfam.

I'm not sure clustering RNAfold predictions with RNAforester will tell you much either. Locarna and CMfinder have been used previously to cluster many ncRNA predictions.

ADD COMMENTlink modified 22 months ago by RamRS27k • written 10.0 years ago by Paul Gardner190

Thank you Paul. I ran the search via the web-site. I know they use a blast pre-filter for speed. I have also tried to run infernal on the CM directly but this takes ages to complete. CMfinder looks very promising too, hope you don't mind i put in some links.

ADD REPLYlink written 10.0 years ago by Michael Dondrup47k

No prob. I would've added links but last time I tried here I was blocked.

ADD REPLYlink written 10.0 years ago by Paul Gardner190
2
gravatar for Jaydon
10.0 years ago by
Jaydon40
Jaydon40 wrote:

BTW, we also do 3' and 5'RACE to confirm the validity of the ends. And you'll be surprise to find alternative splicing variants for most of long candidates.

ADD COMMENTlink written 10.0 years ago by Jaydon40
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