Using MEME from command line

[ahmedel...@gmail.com]

I have a genome sequence and want MAST output file to included in other analysis. I just download pre request and MEME package but I don't know how to analyze   this genome from command line. So, kindly tell me the way to do that.

Thanks in advance.

Bests,

Ahmed

 

[CharlesEGrant]

Hi Ahmed,

We're happy to help with specific questions about using the MEME Suite, but this question is so general that it's not answerable in a few paragraphs. I'd direct you to the documentation for the MEME Suite command line tools. You'll also find some brief summaries here on the MEME Suite Q&A site:

The basics of using MEME to discover motifs

How do I use MEME suite for searching for motifs?

The basics of using FIMO to search for motif occurrences

For more detailed information, you may also want to review some of the papers published for these tools. You can find a list of the relevant papers here.

If you aren't familiar with using the UNIX/Linux command line you'll need to find a local mentor, or review one of the many online introductions. Assistance with basic command line usage is beyond the scope of help we can offer.

Finally, I would offer that MAST is not a tool for genome scale analysis. This question on the MEME Suite Q&A site may be of help:

How does MAST differ from FIMO?

If you have specific questions after reviewing these materials, we'll be happy to try and help.