MOTIF IDENTIFICATION IN RNA SEQUENCES

Question

[vin23]

Hello all, I have a list of upregulated mRNAs in Th2 cells. Can any one suggest a way in which I can identify a conserved motif of these translationally regulated genes so that I can find out a translation factor which binds to these regions. Thank you

[Omics data mining]

Hello I would suggest you to check MEME online webserver. You can use https://meme-suite.org/meme/ for motif identification either from DNA or protein sequence and further annotate them .

I hope it helps

[vin23]

Thank you so much. Will try and see if it works

[vin23]

Hello, So I tried MEME and got some motifs. I am looking for RNA motifs, so I wanted to ask whether we can replace the T (Thymine) in my UTR sequences to U (Uracil) and then search for motifs. Is this an ideal way or there is another way to identify RNA motifs?

[Omics data mining]

In MEME, you can define if sequences are -dna or "-rna" (https://meme-suite.org/meme/doc/meme.html) which would be matched against https://meme-suite.org/meme/doc/alphabet-format.html#standard_RNA for RNA based motif analysis in MEME.

[vin23]

Okay, So when I upload the UTR sequence in the input primary sequence, it itself detects it as DNA. I have downloaded the UTR sequences from UCSC Genome Browser. Once I get the motifs using this I am unable to use TOMTOM for motif comparison since it is detected as DNA and not RNA. I tried changing T to U and then uploading the sequences and it worked as it detected it as RNA sequences and TOMTOM was also able to recognize the MOTIFS as RNA. Even if as suggested that T is permitted for input sequences I am not able to see the results for RNA motifs.