Database and Motifs High-scoring Motif Occurences Debugging Information



FIMO - Motif search tool

FIMO version 4.10.0, (Release date: Tue May 06 16:46:04 2014 +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/sample-dna-Klf1.fa
Database contains 904 sequences, 452000 residues

MOTIFS memechip_example_output_files/dreme_out/dreme.xml (nucleotide)

MOTIF WIDTH BEST POSSIBLE MATCH
GGGYGK 6 GGGTGT
TTATCW 6 TTATCT
AGAWA 5 AGAAA

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


SECTION I: HIGH-SCORING MOTIF OCCURENCES

Motif Sequence Name Strand Start End p-value Matched Sequence

DEBUGGING INFORMATION

Command line:

/Users/cegrant/meme_4.10.0/bin/fimo --parse-genomic-coord --verbosity 1 --oc memechip_example_output_files/fimo_out_1 --bgfile memechip_example_output_files/background --motif GGGYGK memechip_example_output_files/dreme_out/dreme.xml memechip_example_output_files/sample-dna-Klf1.fa

Settings:

output directory = memechip_example_output_files/fimo_out_1 MEME file name = memechip_example_output_files/dreme_out/dreme.xml sequence file name = memechip_example_output_files/sample-dna-Klf1.fa
background file name = memechip_example_output_files/background allow clobber = true compute q-values = true
parse genomic coord. = true text only = false scan both strands = true
max sequence length = 250000000 output threshold = 0.0001 threshold type = p-value
max stored scores = 100000 pseudocount = 0.1 verbosity = 1
selected motif = GGGYGK

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


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