ame [options] <sequence file> <motif file>+
A collection of (primary) sequences in FASTA format. The sequences must be sorted by increasing value of some secondary criterion (e.g., expression level, peak height, fluorescence score). In this documentation, we refer to this secondary criterion as the "FASTA score". This score can optionally be placed in the FASTA ID line. If present, the FASTA score must come immediately after the sequence ID. For example, if the FASTA ID line is
0.123is the FASTA score for that sequence.
File(s) containing MEME formatted motifs. Outputs from MEME and DREME are supported, as well as Minimal MEME Format. You can convert many other motif formats to MEME format using conversion scripts available with the MEME Suite.
AME writes to a directory,
ame_out, unless a different
directory name is specified on the command line. The output directory
contains outputs in two formats: HTML and plain text, in files named
|--control||control file||A collection of control sequences in FASTA format.
If a set of control sequences is provided, AME determines if each motif
is enriched in the primary set compared to the control set.
AME does this by appending the control sequence set to the primary sequence
set and sets
|--method||fisher|ranksum|mhg|4dmhg|spearman|linreg||Select the association function for testing motif enrichment
||The Fisher's Exact test (
|--scoring||avg|max|sum|totalhits||Method of scoring a single sequence for matches to a motif. The score assigned to a sequence
|--bgformat||0|1|2||Select the background source.
||The background specified in the MEME motif file is used.|
|--bgfile||bfile||The file should be in MEME background file format.||Use frequencies based on the motif file or files. See also --bgformat|
|--length-correction||Correct for length bias: subtract expected hits.||No length correction.|
|--pvalue-threshold||pvalue||Threshold to consider single motif hit significant; only used with
||A p-value threshold of 0.0002 is used.|
|--pvalue-report-threshold||pvalue||Corrected p-value threshold for reporting a motif as significantly enriched.||The threshold of 0.05 is used for reporting a motif.|
|--pwm-threshold||score||For the Fisher's exact test only. This is the minimum motif-based sequence score for a sequence to be a 'true positive'.||A minimum motif score of 1 is used to call a sequence a 'true positive'.|
|--fasta-threshold||p-value||For the Fisher's exact test only when
||A maximum FASTA score of 0.001 is used to call a sequence a 'true positive'.|
|--fix-partition||num||Number of positive sequences; the remainder are the negative sequences.||Partition maximization is performed over the (sorted) input sequences. The partition with the lowest p-value is used.|
|--rsmethod||better|quick||Select how to compute the Wilcoxon rank-sum test:
||Use the heuristic version of the test (
|--poslist||pwm|fasta||For partition maximization, test thresholds on either X (motif)
or Y (FASTA score). Only applies for partition maximisation
and for the Ranksum test.
||Use the FASTA score.|
|--log-fscores||For linear regression and Spearman tests only: regress using ln(FASTA score), rather than the score directly.||Use the score directly.|
|--log-pwmscores||For linear regression and Spearman tests only: regress using ln(pwm score), rather than the score directly.||Use the score directly.|
|--normalise-affinity||Normalise motif scores so that motif scores can be compared directly. Only relevant for Spearman and Linear Regression tests, where p-values are not calculated.|
|--linreg-switchxy||Make the x-points FASTA scores and the y-points motif scores. Only relevant for Spearman and Linear Regression tests.||Keep the original axis.|
|--verbose||1|2|3|4|5||A number that regulates the verbosity level of the output information messages. If set to 1 (quiet) then it will only output error messages whereas the other extreme 5 (dump) outputs lots of mostly useless information. This option is best placed first. At verbosity level 3, AME will report the significance of each set of each partition of the sequences that it considers.||The verbosity level is set to 2 (normal).|
|--help||Print a usage message and exit.||Run as normal.|
|--version||Display the version and exit.||Run as normal.|
If you use AME in your research, please cite the following paper:
Robert McLeay and Timothy L. Bailey, "Motif Enrichment Analysis: A unified framework and method evaluation", BMC Bioinformatics, 11:165, 2010, doi:10.1186/1471-2105-11-165. [full text]