## NGS ChIP-seq / Find common motifs and match to JASPAR

### Description

This tool scans a set of genomic regions for consensus sequence motifs, calculates the alignment score against transcription factors in the Jaspar database and finds the 10 highest ranking for each motif.

### Parameters

- P-value cutoff (0...1) [0.0002]
- E-value cutoff (0...1) [0.01]
- Genome ([BSgenome.Hsapiens.UCSC.hg17, BSgenome.Hsapiens.UCSC.hg18, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm8, BSgenome.Mmusculus.UCSC.mm9, BSgenome.Rnorvegicus.UCSC.rn4]) [BSgenome.Hsapiens.UCSC.hg18]

### Details

For a more thorough description of the technical details please consult the original publications cited in the References section below. Briefly, the analysis proceeds through the following steps:

  - Given a set of genomic regions the analysis algorithm will first perform a de novo motif discovery in an unseeded fasion. The starting set of position weighted matrices (PWM) is obtained through a combination of space dyads and expectation maximization procedures. Further optimization is achieved using genetic algorithms techniques.
  - In the second phase of the analysis. the PWM for known transcription factors collected in the JASPAR database, are matched to the set of consensus motifs discovered in the previous step.
  - Finally, the top ten best matching transcription factors are gathered for each consensus motif, logo plots created and E-values scoring the match strength are calculated.

### Output

The analysis output consists of the following:

- motif-analysis-summary.tsv: A test file that summarizes the analysis with information on

  - number of consensus motifs
  - number of matches per motif
  - matches repartition
  - the UPAC nucleotide sequences for the motifs
  - number of occurrences of consensus sequence for each motif
  - the position weighted matrices for each motif

- logo-plot-(...).pdf: For each consensus motif the ten best matching transcription factors from the JASPAR database are represented with a logo plot.

### References

This tool uses the following Bioconductor packages:

- MotIV
- rGADEM
- BSgenome annotation packages

For more details refer to these publications:
S. Mahony, P.V. Benos "STAMP: a web tool for exploring DNA-binding motif similarities." Nucl Acids Res, (2007) 35:W253-258
S Mahony, PE Auron, PV Benos, "DNA familial binding pro les made easy: comparison of various motif alignment and clustering strategies", PLoS Computational Biology (2007) 3(3):e61
L. Leiping. GADEM: A Genetic Algorithm Guided Formation of Spaced Dyads Coupled with an EM Algorithm for Motif Discovery. J Comput Biology, (2009) Feb;16(2):317-29.