Finding a way to automatically screen RNA sequences for possible editing sites

Question

[gabrieldupre28]

Hi!

As a Ph.D. student, I'm working on a very interesting project about the genetic evolution of viral RNA sequences. In this work, I'm looking for possible editing-sites or nucleotide motifs that are favorable to viral polymerase slippage, leading to viral genome evolution. These particular motifs are mostly short repeated sequences (runs of AAA's, TTTT's,...). I've heard about the MEME-suite, but I'm not really familiar with its different options and programs. What would be the best program in the MEME-suite for this research topic? Otherwise, is there other software that can perform automatic motifs-screening of RNA sequences?

Best regards,

Gabriel

[ATpoint]

MEME has an extensive manual page, so does HOMER, another popular motif search tool. I suggest you read them extensively. If things are then still unclear you should be mores specific in your question. Right now the question is essentially how to perform motif search, and the answer would be "use MEME or HOMER". What data do you have to work on?

Answer 1

[gabrieldupre28]

Hi ATpoint,

Thank you for your response. I am using MEME, and after some readings, I am starting to become pretty used to it. Thank you again, Gabriel