This tool is a wrapper for findMotifs.pl from Homer package. By default, this is a promoter-based motif finding analysis, but can also be used to look for RNA motifs in mRNAs or any motifs in sequences within user provided fasta datasets.

The tool requires, at a minimum the input of a list of genes or some fasta sequences to serve as the positive set and the name of the promoter set (i.e. organism). If a background set is not provided, it can be auto-generated from the set of all genes in the DB. By default the tool scans for both the differential enrichment of known motifs that are stored in its DB, as well as de novo discovery of motifs that are disproportionally represented sequences in the input dataset in comparison to the background set.

This program performs a number of operations en route to providing a basic analysis of motif and functional enrichment. The various steps are outlined below:

• Convert Gene IDs to consistent gene identifier (usually Entrez Gene ID).
• Select appropriate background IDs (usually all confident genes, i.e. not olfactory genes), or take user supplied list.
• Perform Gene Ontology enrichment calculation (disabled, refer to other tools such as GoSeq).
• Assign weights to background promoters based on the distribution of CpG content in the target gene promoters such that comparable numbers of low and high-CpG promoters are analyzed.
• Perform de novo motif analysis.
• Create output HTML pages for de novo analysis.
• Perform known motif enrichment analysis and generate corresponding output pages.

If a list of gene identifiers is provided for the positive and/or background, set ensure that the input contains in each line of its first column, either of the following: HOMER accepts a broad range of different types of gene identifiers: * NCBI Entrez Gene IDs * NCBI Unigene IDs * NCBI Refseq IDs (mRNA, protein) * Ensembl Gene IDs * Gene Symbols (i.e. Official Gene names, like "Nfkb1" ) * Popular affymetrix probe IDs (MOE430, U133plus, U95, U75A)