Usage:

ame [options] <sequence file> <motif file>+

Description:

AME (Analysis of Motif Enrichment) scores a set of DNA sequences given a set of DNA-binding motifs, treating each position in the sequence as a the starting point of a possible binding event. AME counts the number of cases where the p-value of the binding event for each motif is below a given threshold, and performs a Fisher exact test versus the number of binding events in a background sequence set to determine the p-value of the count for each motif. The background set is appended to the main sequence set in the input file, and the offset within the file where the background starts is specified on the command line.

A previously described version of AME has a range of options not implemented in this version.

Input:

• <sequence file> is a collection of sequences in FASTA format.
• <motif file> containing a list of motifs, in MEME format. More than one file can be specified.

Output:

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 respectively ame.html and ame.txt.

Options:

• --o <dir name> - Specifies the output directory. If the directory already exists, the contents will not be overwritten.
• --oc <dir name> - Specifies the output directory. If the directory already exists, the contents will be overwritten.
• --bgformat 0..2 - Source for determining background frequencies
  

  0: uniform background
  1: MEME motif file
  2: Background file

• --bgfile <bfile> - Read background frequencies from <bfile>. The file should be in MEME background file format. The default is to use frequencies based on the motif file or files. See also --bgformat
• --length-correction - Correct for length bias: subtract expected hits. Default=no length correction.
• --pvalue-threshold <float, default=2e-4> - Threshold to consider single motif hit significant.
• --fix-partition - Number of positive sequences; the balance are used as the background.
• --pvalue-report-threshold <float, default=1e-3> - Corrected p-value threshold for reporting a motif.
• --verbose <1...5> - Integer describing verbosity (low number is less verbose). Best placed first.
• --help - Print a usage statement.

The default output directory is ame_out, and is not overwritten (i.e., the default is the same as --o ame_out).

Notes

This version of AME does not implement a number of alternative scoring modes previously described. In the version, only Fisher exact test and total hits modes are implemented, with a fixed partition between foreground and background sequences. fix-partition in this version is therefore required rather than optional.

Citing ame

If AME is of use to you in your research, please cite:

Robert C. McLeay, Timothy L. Bailey (2009).
"Motif Enrichment Analysis: a unified framework and an evaluation on ChIP data."
BMC Bioinformatics 2010, 11:165, doi:10.1186/1471-2105-11-165.

Contact the authors

You can contact the authors via email:

Robert McLeay r.mcleay@imb.uq.edu.au, and Timothy Bailey t.bailey@imb.uq.edu.au.

Bug reports should be directed to Robert McLeay.