What tools can use to find RNA modification sites?
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6.3 years ago

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.

myposts RNA-Seq SNP • 1.5k views
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Hello, in fact you will find it in many edu-site, here is a RNA modificaion database : http://rna.rega.kuleuven.be/ssu/

it's quick and convinient 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!

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6.2 years ago
lsp03yjh ▴ 810

You can use RMBase(http://mirlab.sysu.edu.cn/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.

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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.

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