What tools can use to find RNA modification sites?

Question

[guillermofernandeznegrete]

Hi I'm trying to predict modified ribonucleotides sites under stress condition bioinformaticly and I don't know what tool could I use. Any suggestion.

[sherrycd525]

Hello, in fact you will find it in many edu-site, here is a RNA modification database: http://rna.rega.kuleuven.be/ssu/

It's quick and convenient you just browse your data, and some information and data you can download here: http://rnaedit.com/download/ or you can choose RNA analysis service: http://www.cd-genomics.com/RNA-Seq-Transcriptome.html

Hope this will be useful for you!

Answer 1

[lsp03yjh]

You can use RMBase to find RNA modification sites identified from 404 transcriptome sequencing datasets (Pseudo-seq, Ψ-seq, CeU-seq, Aza-IP, MeRIP-seq, m6A-seq, miCLIP, m6A-CLIP, RiboMeth-seq). It contains more than 100 modification types, such as m6A, m5C, 2'-O-Me and pseudouridine etc.

[gufernandez10]

thanks it's a good approximation and useful in mm10 that I'm studying, but I'm looking for something more specific, maybe a software that find this specific modification sites. Now I'm find a software names HAMR (high trhoughput....) that find modified nucleotides.