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We process your sequences through a series of steps to help you identify motifs in your DNA sequences.

If you use MEME-ChIP in your research, please cite the following paper:
Philip Machanick and Timothy L. Bailey, "MEME-ChIP: motif analysis of large DNA datasets", Bioinformatics, 2712, 1696-1697, 2011.

For more detail, see this Tutorial. You may find it helpful to open it in another window while examining your results.

## Results

MEME output: | HTML | plain text | XML | Motifs discovered in 600 (randomly chosen) trimmed (central 100bp) input sequences.
TOMTOM output: | HTML | plain text | XML | Motifs from JASPAR CORE 2009 that match motifs MEME discovers.
MAST output: | HTML | plain text | XML | Predicted locations of all MEME motifs (p < 0.0001) in the input sequences.
AMA output: |  | plain text | XML | Estimated binding affinity of each MEME motif to each input sequence.
DREME output: | HTML | plain text | XML | Motifs discovered in the trimmed (central 100bp) input sequences.
TOMTOM output: | HTML | plain text | XML | Motifs from JASPAR CORE 2009 that match motifs DREME discovers.
MAST output: | HTML | plain text | XML | Predicted locations of all DREME motifs (p < 0.0001) in the input sequences.
AMA output: |  | plain text | XML | Estimated binding affinity of each DREME motif to each input sequence.
AME output: | HTML | plain text |  | Motifs from JASPAR CORE 2009 enriched in the trimmed (central 100bp) input sequences.
CENTRIMO output: | HTML | plain text |  | MEME and DREME motif centrality in the input sequences. The HTML results require a modern browser with full canvas support.

## Data

Input Sequences: | sample-dna-Klf1.fa |  |  | Your original untrimmed sequences.
fasta-center output: | seqs-centered |  |  | Your sequences centered and trimed to width 100.
fasta-dinucleotide-shuffle output: | seqs-shuffled |  |  | The centered sequences randomly shuffled maintaining their dinucleotide frequency, used as a background for DREME and AME.
AME input: | seqs-centered_w_bg |  |  | The centered sequences followed by the same sequences after dinucleotide shuffling.
fasta-subsample (used) output: | seqs-sampled |  |  | A random sample of 600 of the centered sequences, used by MEME.
fasta-subsample (discarded) output: | seqs-discarded |  |  | The centered sequences omitted from the sample used by MEME.

## Commands

mkdir memechip_out fasta-center -len 100 < sample-dna-Klf1.fa > memechip_out/seqs-centered fasta-dinucleotide-shuffle -f memechip_out/seqs-centered -t -dinuc > memechip_out/seqs-shuffled cat memechip_out/seqs-centered memechip_out/seqs-shuffled > memechip_out/seqs-centered_w_bg fasta-subsample memechip_out/seqs-centered 600 -rest memechip_out/seqs-discarded > memechip_out/seqs-sampled meme memechip_out/seqs-sampled -oc memechip_out/meme_out -dna -mod zoops -nmotifs 3 -minw 6 -maxw 30 -revcomp -nostatus tomtom -verbosity 1 -oc memechip_out/meme_tomtom_out -min-overlap 5 -dist pearson -evalue -thresh 0.1 -no-ssc memechip_out/meme_out/meme.txt JASPAR_CORE_2009.meme mast -oc memechip_out/meme_mast_out memechip_out/meme_out/meme.txt sample-dna-Klf1.fa -ev 820 -nostatus ama --verbosity 1 --oc memechip_out/meme_ama_out --sdbg 0 memechip_out/meme_out/meme.txt sample-dna-Klf1.fa dreme -v 1 -oc memechip_out/dreme_out -p memechip_out/seqs-centered -n memechip_out/seqs-shuffled -png tomtom -verbosity 1 -oc memechip_out/dreme_tomtom_out -min-overlap 5 -dist pearson -evalue -thresh 0.1 -no-ssc memechip_out/dreme_out/dreme.txt JASPAR_CORE_2009.meme mast -oc memechip_out/dreme_mast_out memechip_out/dreme_out/dreme.txt sample-dna-Klf1.fa -ev 820 -nostatus ama --verbosity 1 --oc memechip_out/dreme_ama_out --sdbg 0 memechip_out/dreme_out/dreme.txt sample-dna-Klf1.fa ame --verbose 1 --oc memechip_out/ame_out --fix-partition 820 --bgformat 0 memechip_out/seqs-centered_w_bg JASPAR_CORE_2009.meme centrimo -verbosity 1 -oc memechip_out/centrimo_out sample-dna-Klf1.fa memechip_out/meme_out/meme.txt memechip_out/dreme_out/dreme.txt