FIMO version 4.11.4, (Release date: Thu Mar 30 17:02:08 2017 -0700)

For further information on how to interpret these results or to get a copy of the FIMO software please access http://meme.nbcr.net

If you use FIMO in your research, please cite the following paper:
Charles E. Grant, Timothy L. Bailey, and William Stafford Noble, "FIMO: Scanning for occurrences of a given motif", Bioinformatics, 27(7):1017-1018, 2011. [full text]

• There were 652 motif occurences with a p-value less than 0.0001. The full set of motif occurences can be seen in the tab-delimited plain text output file fimo.txt, the GFF file fimo.gff which may be suitable for uploading to the UCSC Genome Table Browser (assuming the FASTA input sequences included genomic coordinates in UCSC or Galaxy format), or the XML file fimo.xml.
• The p-value of a motif occurrence is defined as the probability of a random sequence of the same length as the motif matching that position of the sequence with as good or better a score.
• The score for the match of a position in a sequence to a motif is computed by summing the appropriate entries from each column of the position-dependent scoring matrix that represents the motif.
• The q-value of a motif occurrence is defined as the false discovery rate if the occurrence is accepted as significant.
• The table is sorted by increasing p-value.

Command line:

/net/noble/vol1/home/cegrant/meme_4.11.4/bin/fimo --parse-genomic-coord --verbosity 1 --oc memechip_example_output_files/fimo_out_1 --bgfile memechip_example_output_files/background --motif WGGGTGTGGYYS memechip_example_output_files/meme_out/meme.xml memechip_example_output_files/Klf1.fna

Settings:

  

    
output_directory = memechip_example_output_files/fimo_out_1
    
MEME file name = memechip_example_output_files/meme_out/meme.xml
    
sequence file name = memechip_example_output_files/Klf1.fna
  
  

    
background file name = memechip_example_output_files/background
    
alphabet = DNA
    
max stored scores = 100000
  
  

    
allow clobber = true
    
compute q-values = true
    
parse genomic coord. = true
  
  

    
text only = false
    
scan both strands = true
    
max strand = false
  
  

    
threshold type = p-value
    
output theshold = 0.0001
    
pseudocount = 0.1
  
  

    
alpha = 1
    
verbosity = 1
    

  

This information can be useful in the event you wish to report a problem with the FIMO software.