Database and Motifs | High-scoring Motif Occurences | Debugging Information

FIMO - Motif search tool

FIMO version 4.11.1, (Release date: Fri Apr 22 11:12:17 2016 +1000)

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]

DATABASE AND MOTIFS

DATABASE memechip_example_output_files/Klf1.fna
Database contains 904 sequences, 452000 residues

MOTIFS memechip_example_output_files/dreme_out/dreme.xml (DNA)

MOTIF | WIDTH | BEST POSSIBLE MATCH
--- | --- | ---
MCRCCCW | 7 | ACACCCA
TTATCW | 6 | TTATCT

Random model letter frequencies (memechip_example_output_files/background):
A 0.256 C 0.244 G 0.244 T 0.256

SECTION I: HIGH-SCORING MOTIF OCCURENCES

- There were 0 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.

Motif | Sequence Name | Strand | Start | End | p-value | q-value | Matched Sequence
--- | --- | --- | --- | --- | --- | --- | ---

DEBUGGING INFORMATION

Command line:

    /Users/t.bailey/meme_hg/meme/BUILD/bin/fimo --parse-genomic-coord --verbosity 1 --oc memechip_example_output_files/fimo_out_2 --bgfile memechip_example_output_files/background --motif TTATCW memechip_example_output_files/dreme_out/dreme.xml memechip_example_output_files/Klf1.fna

Settings:

        output_directory = memechip_example_output_files/fimo_out_2
        MEME file name = memechip_example_output_files/dreme_out/dreme.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.

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