AME - Submission form

Choose whether or not to provide control sequences to AME.

If you choose "Shuffled input sequences", AME will create control sequences for you by shuffling the letters in each of your input sequences, preserving 2-mers.

If you provide control sequences, they should have a similar length distribution to that of your primary sequences or motif enrichment p-values will be inaccurate.

If you choose "NONE", then AME will assume that your sequences are either sorted according to some secondary criterion, or that they each contain a number (a 'FASTA score') in their FASTA header line. AME will sort your sequences in increasing order of FASTA score and compute the enrichment of each motif in sequences at the beginning of the sorted list. The FASTA header line should have the format:

>seq_name fasta_score other_text

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Use the menu below to choose how you wish to input your primary sequences.

Note 1: The sequences may have differing lengths.

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Use the menu below to choose how you wish to input your control sequences.

Note 1: The sequences may have differing lengths.

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Using the menu below, select the way you want to input motifs that will be tested for enrichment in your input sequences. Use the first menu below to choose how you want to input the motifs, and the second menu to choose the particular motif database you require.

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Select the statistical test for testing motif enrichment.

- Fisher's exact test - one-tailed Fisher's exact test (1)
- Ranksum test - one-tailed Wilcoxon rank-sum test, also known as the Mann-Whitney U test (1)
- Pearson CC - significance of the correlation of sequence PWM scores and FASTA scores (3)
- Spearman CC - significance of the correlation of sequence PWM score ranks and FASTA score ranks
- 3dmhg - 3-dimensional multi-hypergeometric test (2)
- 4dmhg - 4-dimensional multi-hypergeometric test (2)

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(1) These tests allow control sequences.

(2) These tests require the "totalhits" sequence scoring method.

(3) This test requires FASTA scores in the sequence header lines.

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Choose how a single sequence is scored for matches to a single motif. The 'PWM score' assigned to a sequence is either:

- Average odds score - the average PWM motif score of the sequence (note: 'motif scores' are odds scores, not log-odds scores as in some other MEME Suite tools)
- Maximum odds score - the maximum motif score of the sequence
- Total odds score - the sum of the motif scores of the sequence
- Total hits - the total number of positions in the sequence whose motif score is greater than the "hit threshold" for the motif

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The "hit threshold" for a motif is defined as this fraction times the maximum possible log-odds score for the motif. A position is considered a "hit" if the log-odds score is greater than or equal to the "hit threshold".

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Threshold for reporting enriched motifs. Only motifs with enrichment E-values no greater than this number will be reported in AME's output. (The E-value is the motif p-value multiplied by the the number motifs in the input.)
Reduce the threshold value if you want AME to report fewer, more significantly enriched motifs. Set the threshold value to the total number of motifs in your input if you want AME to report the enrichment of all input motifs.

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Select the size of the k-mer to preserve the frequencies of when shuffling the letters of sequences to create the background sequences. Selecting a value of 1 may work better than the default (kmer=2) in some cases. Be wary of setting the k-mer to less than 2 if the primary sequences contain long runs of a single letter, as is the case with repeat-masked sequences.

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The background model normalizes for biased distribution of single letters in the sequences. By default AME will create a 0-order Markov sequence model from the letter frequencies in the primary sequences. You may also choose to use a uniform background model or to use the background model specified by the motifs.

Alternately you may select "Upload background" and input a file containing a background model.

The downloadable version of the MEME Suite contains a program named "fasta-get-markov" that you can use to create background model files in the correct format from FASTA sequence files.

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AME - Analysis of Motif Enrichment
../doc/images/ame_icon.png: AME Logo

Data Submission Form

Perform standard (non-local) motif enrichment analysis.

## Select the type of control sequences to use

Shuffled input sequences User-provided control sequences NONE

alphabet
sequence alphabet register_component

sequences sequences Input the primary sequences Enter the sequences in which you want to find enriched motifs. FILE register_component
control_sequences control sequences Input the control sequences Enter the control sequences. FILE register_component
motifs motifs Input the motifs Select a motif database or enter the motifs you wish to test for enrichment. DATABASE register_component

## Select the sequence scoring method

## Select the motif enrichment test

### Choose the (fractional) score threshold for hits

Fraction of maximum log-odds

### Set the E-value threshold for reporting enriched motifs

E-value ≤

### Shuffling preserves frequencies words of what size?

Word size:
background DNA zero register_component