Meta-MEME motif search tools

Meta-MEME provides a suite of programs for searching a sequence database for occurrences of a known collection of motifs. The programs can search DNA or protein databases, and can search for individual motifs, or for ordered series or unordered clusters of motifs.

Inputs:

Each program takes as input a collection of DNA or protein motifs in an XML format, and a databse of sequences in FASTA format.

Outputs:

An XML file using the CisML schema.

General options (available in all programs)

A number of options are available for each of the programs. Some of the options may be used with any of the programs:

Program specific options

Other options are specific to the individual program. This table describes which options are available for which programs.

Other Tools

The Meta-MEME software distribution also includes the following other programs:

Additional documentation is available concerning

Sample output files are available for

Installation instructions.

Release notes.

Visit the Meta-MEME home page at the San Diego Supercomputer Center.

The programs are:

Meta-MEME was developed by William Stafford Noble in the Department of Genome Sciences the University of Washington, and by Timothy Bailey at the University of Queensland, with input from Charles Elkan in the Department of Computer Science and Engineering at the University of California, San Diego and Michael Gribskov at the San Diego Supercomputer Center. Meta-MEME is funded by the National Biomedical Computation Resource.

Copyright information. Please send comments and questions to Charles Grant at cegrant@u.washington.edu