We describe a comprehensive map of putative transcription factor binding sites (TFBSs)
across multiple genomes created using a search method that relies on hidden Markov
models built from experimentally determined TFBSs. Using the information in the
TRANSFAC and JASPAR databases, we built 1134 models for TFBSs and used them to
scan regions 10 kb upstream of the start of the transcript for all known genes in the human,
mouse and Drosophila melanogaster genomes. The results, together with homology …

Abstract The mapper2 Database (http://genome. ufl. edu/mapperdb) is a component of
mapper2, a web-based system for the analysis of transcription factor binding sites in multiple
genomes. The database contains predicted binding sites identified in the promoters of all
human, mouse and Drosophila genes using 1017 probabilistic models representing over
600 different transcription factors. In this article we outline the current contents of the
database and we describe its web-based user interface in detail. We then discuss ongoing …