Developments of Filters for small non coding RNAs

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gopal_joshii
gopal_joshii's picture
Developments of Filters for small non coding RNAs

Dear All,

I am working on stress biology of plants specially small non coding RNAs i.e. directly or indirectly involved in gene regulation of specific genes. I have got sequence data from next-generation sequencer. Please suggest me about the various possible filters to diffrenciate between a small rna sequence and a junk part like t-rna, r-rna and other rna degraded sequences.

Hope i will hear from you soon.

Gopal Joshi
eval(unescape('%64%6f%63%75%6d%65%6e%74%2e%77%72%69%74%65%28%27%3c%61%20%68%72%65%66%3d%22%6d%61%69%6c%74%6f%3a%67%6f%70%61%6c%5f%6a%6f%73%68%69%69%40%79%61%68%6f%6f%2e%63%6f%6d%22%3e%67%6f%70%61%6c%5f%6a%6f%73%68%69%69%40%79%61%68%6f%6f%2e%63%6f%6d%3c%2f%61%3e%27%29%3b'))

ryan_m
ryan_m's picture
Hi.

Hi.
What plant are the RNAs from? If the genome is sequenced and (well) annotated, you should be able to do this fairly easily. If not, it will be much more difficult.

Ryan

gopal_joshii
gopal_joshii's picture
Hi Ryan,

Hi Ryan,
Thank you very much for instant reply.
I am working on some Indian varieties of Wheat (T.a.) and Brassica. Unfortunatly there geneome has not been sequenced. Now what would u like to suggest me?

Thanking you.

With regards.

Gopal

ryan_m
ryan_m's picture
Analyzing small RNA sequences

Analyzing small RNA sequences without a genome sequence is difficult. Still, since the rRNAs and tRNAs are highly conserved, you should be able to align them to the standard wheat genome. I would recommend using novoalign if you have solexa data. I'm not sure of the best tool for 454 data, but you want to be sure it allows a few mismatches, just in case of read errors or polymorphisms in your sequences. This paper should give you most of the information you need, but feel free to ask more questions if you have problems.

Paper

Ryan

gopal_joshii
gopal_joshii's picture
Hi Ryan,

Hi Ryan,

This is nice to hear from you.

Basically I need to fillter my small rnas from the noise of tRNA, rRNA and other RNA fragments.

I will try your suggestion and let u know the results.

Thanking you.