The basics of using FIMO to search for motif occurrences

[CharlesEGrant]

FIMO is a tool for searching for occurrences of motifs in DNA and proteins. This is a very brief summary of how to use the public FIMO web application to search for motif occurrences in your sequence data.

1.  Open the FIMO web application in your web browser.

2. Either enter your motifs directly or select the name of the file containing your motif(s) in the section labeled "Input the motifs".

3. Select the sequence database FIMO should use: 

• Many common sequence databases are pre-loaded on the FIMO server. Select the database category from the drop down list labeled "Category", then select the name of the database in the drop down list labeled "Database". 
  
• Alternatively, you can upload your own sequence database. This must be in the form of a plain text FASTA file.  Select the name of the file containing your sequence database in the box labeled "Your FASTA sequence file". Note that uploads are limited to 80Mb.
  

4. Optionally, you may adjust the p-value threshold for motif occurrences. Motif matches whose p-value is greater than this threshold will not be shown in the results. When searching whole genomes you should choose a very stringent threshold to avoid your results being overwhelmed with chance matches. The default p-value threshold is 1e-4.

5. You may optionally provide your email address. This will only be used to send you a link to your job results. 

6. Click on the "Start Search" button". 

 

Important things to know:

• The public FIMO web application limits the size of uploaded sequence files to 1Mb. If you need to analyze a larger file you'll need to install the FIMO software locally.
• The motif file and uploaded sequence file must be in plain text. The FIMO application is unable to process Microsoft Word files or compressed files. See Why can't the MEME Suite read my sequence data? for more information. The motif file must be in the MEME motif format
  
• Jobs running longer than two hours will be halted.
• Completed jobs are kept on the web site for 3 days. Be sure to download your results before they are removed!

Information about the command line version of FIMO can be found in the FIMO command line documentation.

Information about how FIMO works can be found in this paper.

For a brief overview of the other tools in the MEME Suite see How do I use MEME suite for searching for motifs?

[Fasemore MANDELA]

How do i make fimo only search with the + strand of a given motif generated with MEME?

[CharlesEGrant]

If you are using the command line version of FIMO you can use the ‘--norc’ option. This option is described in the documentation for the command line version of FIMO:

http://meme-suite.org/doc/fimo.html


If you are using the FIMO web application, Click on the “Advanced Options” button, and then click on the check box titled "scan given strand only”.

[Malcolm Cook]

link rot at:  FIMO command line documentation.

[cegrant]

Thanks for spotting the problem and letting us know about it! It should be fixed now.