Question: Problems to find over-represented TFBS with TOUCAN software
gravatar for CiAlves
2.0 years ago by
Brazil/University of São Paulo
CiAlves0 wrote:

Hi, please, can anybody help me? Recently I downloaded the TOUCAN software last version to identify transcription factor-binding sites in different haplotypes (sequences) originated from mutations in the promoter region of a single gene (Human). This is my first time using this software. I am using the MotifScanner algorithm to search for potential TFBS in a set of target sequences using the TRANSFAC database and as model background the Human_DBTSS_promoter (0). Until here it's ok, but after, we use the MotifScanner output to perform binominal statistics function of TOUCAN to identify over-represented TFBS. For this purpose, "files with expected frequencies of motif instances in several (sub-)genomes, to be used in the binomial analysis, can either be downloaded from our website or created from local sequence sets within TOUCAN" it is described in the paper "TOUCAN 2: the all-inclusive open source workbench for regulatory sequence analysis, Nucleic Acids Res (2005) 33 (suppl_2): W393-W396. But I can't find this frequencies files in the nor in the Do anybody work with TOUCANt can help me? Where can I find these type of file to perform the statistical analysis or how to do an annoted reference set once I am working with the promoter region?

Best regards, Cinthia

ADD COMMENTlink modified 2.0 years ago by genomax62k • written 2.0 years ago by CiAlves0
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