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HOMER Motif Finder Specifications

Process Details

  • Name: HOMER Motif Finder
  • Process UUID: 5d137b1927af40818ef36776665aaf2d
  • Process Group: Misc.

Overview

HOMER Motif Finder is a computational process designed to identify enriched sequence motifs within genomic regions of interest. This tool performs comprehensive motif discovery by analyzing both known motifs from databases and discovering novel de novo motifs in the provided genomic coordinates. The process is particularly useful for identifying transcription factor binding sites and regulatory elements in ChIP-seq peaks, accessible chromatin regions, or other genomic intervals.

This process is implemented in Bash, which invokes the HOMER (Hypergeometric Optimization of Motif EnRichment) suite for motif analysis.

Key Functionality

  • De novo motif discovery: Identifies novel sequence motifs enriched in the input genomic regions using statistical optimization algorithms
  • Known motif enrichment analysis: Compares input sequences against comprehensive databases of known transcription factor binding motifs
  • Customizable motif parameters: Allows adjustment of motif length, search window size, optimization parameters, and search constraints
  • Strand-specific analysis: Provides options for single-strand or bidirectional motif searching
  • RNA motif support: Includes specialized analysis modes for RNA-binding protein motifs

Input/Output Specification

Inputs

Required Inputs

  • directory

    • Description: Reference directory containing HOMER database files and configuration
    • Format: directory

  • bedFile

    • Description: Genomic coordinates in BED format specifying regions for motif analysis
    • Format: bed

Outputs

  • directory
    • Description: Output directory containing motif analysis results including motif logos, enrichment statistics, and detailed reports
    • Format: directory

Parameters & Settings

These parameters can be adjusted in the Foundry UI when running this process.

  • Motif length

    • Description: Motif length, default=8,10,12 [NOTE: values greater 12 may cause the program to run out of memory - in these cases decrease the number of sequences analyzed (-N)
    • Default value: 8,10,12

  • Motif size

    • Description: Fragment size to use for motif finding, default=200
      -size <#,#> (i.e. -size -100,50 will get sequences from -100 to +50 relative from center)
      -size given (uses the exact regions you give it, recommended to use same sized regions)
    • Default value: 200

  • Optimize motif finding

    • Description: Number of motifs to optimize, default: 25
    • Default value: 25

  • Mismatches

    • Description: Global optimization: searches for strings with # mismatches, default: 2
    • Default value: 2

  • Output RNA motifs

    • Description: Output RNA motif logos and compare to RNA motif database, automatically sets -norevopp
    • Default value: false

  • No reverse strand search

    • Description: Do not search the reverse strand for motifs, check to prevent reverse search
    • Default value: false

  • No de novo motif search

    • Description: Don't search for de novo motif enrichment, check to prevent de novo search
    • Default value: false

  • No known motif search

    • Description: Don't search for known motif enrichment, check to prevent known motif search
    • Default value: false

References & Resources

  • Tool Documentation: Contact the team for details on findMotifsGenome.pl
  • Related Papers: Heinz, S., Benner, C., Spann, N., Bertolino, E., Lin, Y.C., Laslo, P., Cheng, J.X., Murre, C., Singh, H., and Glass, C.K. (2010). Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Molecular Cell 38, 576-589. DOI: 10.1016/j.molcel.2010.05.004