This tools retrieves promoter sequences for a set of genes and finds shared sequence motifs in them. Currently the tool works only for human, mouse, rat, drosophila and yeast genes.
This tool retrieves upstream sequences for the specified genes and submits them to the Cosmo 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 Small 1000 bp 1000 bp 1000 bp 1000 bp 500 bp Medium 2000 bp 2000 bp 2000 bp 2000 bp 1000 bp Large 5000 bp 5000 bp 5000 bp 5000 bp 2500 bp
After retrieving the promoter sequences, they are submitted to the Cosmo program that finds common motifs (putative transcription factor binding sites). Cosmo can find motifs of two different sizes: small (6-8 nucleotides) and large (10 nucleotides). In addition, the user can define whether both strands of DNA should be searched for the common motifs, whether the motif should appear more than once in a sequence, and what proportion of the sequences should contain the motif.
Cosmo returns common motifs written to a text file. These can then be further analyzed to verify whether they are known transcription factor binding sites. Cosmo also returns an image file containing a sequence logo representation of the motif, and another image showing the location of the motifs.
This tool uses the Bioconductor package Cosmo. Please cite the article:
O. Bembom, S. Kele¸s, and M.J. van der Laan. Supervised detection of conserved motifs in DNA sequences with cosmo. Statistical Applications in Genetics and Molecular Biology: Vol. 6 : Iss. 1, Article 8. URL http://www.bepress.com/sagmb/vol6/iss1/art8.
The use of this tool is allowed for research purposes only.