We have released an important update to the MAPPER server. MAPPER should now be significantly faster and more reliable. As always, please use the Feedback link above to report bugs or unexpected behaviors.

Note: As a consequence of this update, we were forced to temporarily remove access to saved hitsets. They will reappear in your My Hitsets page in the next few days. We apologize for any inconvenience. If you have an urgent need for a saved hitset, please contact us directly.

Welcome to MAPPER

MAPPER is a platform for the computational identification of transcription factor binding sites (TFBSs) in multiple genomes, that combines TRANSFAC® and JASPAR data with the search power of profile hidden Markov models (HMMs). MAPPER incorporates HMMs for all the transcription factors listed in this table.

The MAPPER system is composed of three modules, described below: the MAPPER Database, the Search Engine, and rSNPs. To use MAPPER you should create an account, that will give you the ability to save your results and retrieve them at a later time. Accounts are free for academic and non-commercial purposes. If you would rather use MAPPER without creating an account, please use guest as the username and leave the password field empty.

The MAPPER Database

The MAPPER Database contains putative Transcription Factor Binding Sites (TFBSs) located in the upstream sequences of genes from the human, mouse and D.melanogaster genomes. For each transcript, the region scanned extends from 10,000bp upstream of the transcript start to 50bp downstream of the coding sequence start. Therefore, the database contains putative binding sites in the gene promoter and in the initial introns and non-coding exons.

Information displayed for each putative binding site includes the transcription factor name, its position (absolute on the chromosome, or relative to the gene), the score of the prediction, and the region of the gene the site belongs to. If the selected gene has homologs in any of the other two organisms, the program optionally displays the putative TFBSs in the homologs.

Enter the MAPPER Database or log in with your MAPPER account.

If you use this program for your research please cite:

Marinescu, V. D., Kohane, I. S., and Riva, A. (2005). The MAPPER database: a multi-genome catalog of putative transcription factor binding sites. Nucleic Acids Res 33 (Database Issue), D91-97.

The MAPPER Search Engine

The MAPPER Search Engine allows the identification, visualization and selection of putative TFBSs occurring in the promoter or other regions of a gene from the human, mouse, D.melanogaster, C.elegans or S.cerevisiae genomes. In addition, it allows the user to upload a sequence to query and to build a model by supplying a multiple sequence alignment of binding sites for a transcription factor of interest. Detailed information on this method and on the models used is available in the paper below and its Supplementary Material that can be accessed here.

Enter the MAPPER Search Engine or log in with your MAPPER account

If you use this program for your research, please cite:

Marinescu, V. D., Kohane, I. S., and Riva, A. (2005). MAPPER: a search engine for the computational identification of putative transcription factor binding sites in multiple genomes BMC Bioinformatics 2005, 6(1):79.


rSNPs MAPPER is designed to identify Single Nucleotide Polymorphisms (SNPs) that may have an effect on the presence of one or more TFBSs. The input to rSNPs can consist of one or more genes, a genomic region, or a user-provided sequence. SNPs may be downloaded from dbSNP, entered manually by the user, or obtained by comparing two sequences. The result is a list of TFBSs whose score changes significantly as a consequence of the allele substitution caused by the SNP.

Enter rSNPs MAPPER or log in with your MAPPER account