## Promoter analysis / ClusterBuster

### Description

Retrieves promoter sequences and finds clusters of putative transcription factor binding sites in them. Transcription factor binding sites are searched for using the matrices from the JASPAR library.

### Parameters

- Species (human, mouse, rat, drosophila, yeast) [human]
- Promoter size (short, medium, long) [short]
- Cluster score threshold [5]
- Motif score threshold [6]
- Expected distance between motifs in a cluster [35]
- Range for counting nucleotide frequencies [100]
- Pseudocounts [0.375]

### Details

This tool retrieves upstream sequences for the specified genes and submits them to the ClusterBuster program. It needs to access the chip-specific annotations, so if you have not specified the chiptype during normalization of, e.g., Illumina data, it will not work. RefSeq IDs are used for retrieving promoter sequences constructed and annotated by UCSC genome browser staff. The same promoter sequences can be downloaded as a single FastA-formatted file from UCSC Golden Path folder. User can define how long promoter sequences are used for the analysis:

    		Human		Mouse		Rat		Drosophila	Yeast
    Short		1000 bp		1000 bp		1000 bp		1000 bp 	500 bp
    Medium		2000 bp		2000 bp		2000 bp		2000 bp		1000 bp
    Long		5000 bp		5000 bp		5000 bp		5000 bp		2500 bp

### Output

A text file detailing the cluster of TFBSs found, and their significance. The cluster are marked in the sequences with capital letters.

### Reference

Frith et al (2003) Nuc Acids Res, 31(13):3666-8