How to use Rfam 12.1 to filter rRNA, tRNA in Arabidopsis

Question

[Liquan]

Hi:

Right now I'm doing small RNA analysis using Rfam to filter tRNA, rRNA, etc. But I can't use the newest version 12.1 to find the data to map.

I want to do Bowtie or bwa to filter. But I can't find the fasta file I nee.

Can anybody figure me out?

Thanks!

Answer 1

[natasha.sernova]

The program you need:

https://xfam.wordpress.com/2016/04/27/rfam-12-1-has-been-released/

You said, you cannot use it. OK.

These sites below may help you with data:

http://plants.ensembl.org/info/website/ftp/index.html -

find Arabidopsis thaliana there, you will see many files in different formats

If you click Arabidopsis thaliana - link, you will come here:

http://plants.ensembl.org/Arabidopsis_thaliana/Info/Index

The site also looks helpful. For example, look at the right bottom corner, there some other general links in it.

Other sites with details:

https://www.arabidopsis.org/tools/bulk/sequences/

http://www.plantgdb.org/AtGDB/

[Liquan]

Hi, natasha:

Thanks for your information very much. I think this do me great favor, especially the ensembl data as to Arabidopsis.

However, in order to filter rRNA, tRNA, snRNA and sno RNA, I'd like to use the data in Rfam and extract them from the data.

Have you ever done this before? Actually I don't know how to use Rfam.

Thanks sincerely!

Answer 2

[natasha.sernova]

Dear Liquan,

Try these sites and read the paper in the middle.

http://www.ebi.ac.uk/training/online/courseogs/rfam-quick-tour

http://www.ebi.ac.uk/training/online/

http://rnacentral.org/expert-database/rfam

http://rfam.xfam.org/

The paper:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383904/

By the way, it was cited about 50 times, it seems to be a good idea to look at these articles as well.

Good luck!

P.S. My colleagues used the program, but for other organisms.

[natasha.sernova]

how other people answered your question before:

Biostars.org-post:

Question about bowtie

papers:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4660826/

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4790866/

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4209997/

http://www.nature.com/ncomms/2014/141111/ncomms6443/full/ncomms6443.html