PEAKS

POSITIONAL FOOTPRINTING WEB SERVER

Positional Footprinting

Bellora, N., Farré, D., and Albà, M.M. (2006)
PEAKS: Identification of regulatory motifs by their position in DNA sequences.
Bioinformatics. 2006 Nov 10; [Epub ahead of print]
PEAKS, positional footprinting server.

Transcription factor binding sites libraries

Messeguer, X., Escudero, R., Farré, D., Núñez, O., Martinez, J. and Alba, M.M. (2002)
PROMO: detection of known transcription regulatory elements using species-tailored searches.
Bioinformatics, 18, 333-334.
PROMO (v3.0)

Sandelin, A., Alkema, W., Engstrom, P., Wasserman, W.W. and Lenhard, B. (2004)
JASPAR: an open-access database for eukaryotic transcription factor binding profiles.
Nucleic Acids Res., 32, D91-94.
JASPAR 2005

Matys, V., Fricke, E., Geffers, R., Gossling, E., Haubrock, M., Hehl, R., Hornischer, K., Karas, D., Kel, A.E., Kel-Margoulis, O.V. and et al. (2003)
TRANSFAC: transcriptional regulation, from patterns to profiles.
Nucleic Acids Res., 31, 374-378.
TRANSFAC (v.7.0)

Harbison, C., Gordon, D., Lee, T., Rinaldi, N., Macisaac, K., Danford, T., Hannett, N., Tagne, J., Reynolds, D., Yoo, J., Jennings, E., Zeitlinger, J., Pokholok, D., Kellis, M., Rolfe, P., Takusagawa, K., Lander, E., Gifford, D., Fraenkel, E. and Young, R. (2004)
Transcriptional regulatory code of a eukaryotic genome.
Nature, 431, 99-104.
Yeast regulators binding sites

Fornes O, Castro-Mondragon JA, Khan A, et al.
JASPAR 2020: update of the open-access database of transcription factor binding profiles.
Nucleic Acids Res. 2020; 48(D1):D87-D92.
JASPAR 2020

Promoter databases

Schmid, C.D., Périer, Praz, V., R., Bucher, P. (2006)
EPD in its twentieth year: towards complete promoter coverage of selected model organisms.
Nucleic Acids Res.34, D82-5.
EPD, The Eukaryotic Promoter Database

Zhu, J and Zhang, M.Q. (1999)
SCPD: a promoter database of the yeast Saccharomyces cerevisiae.
Bioinformatics, Vol 15, 607-611
SCPD, The Promoter Database of Saccharomyces cerevisiae

Gene datasets

Mewes, H.W., Frishman, D., Guldener, U., Mannhaupt, G., Mayer, K., Mokrejs, M., Morgenstern, B., Munsterkotter, M., Rudd, S. and Weil, B. (2002)
MIPS: A database for genomes and protein sequences.
Nucleic Acids Res., 30, 31-34.
MIPS Comprehensive Yeast Genome Database (CYGD)

Benson, D.A., Karsch-Mizrachi, I., Lipman, D.J., Ostell, J. and Wheeler, D.L. (2005)
GenBank.
Nucleic Acids Res. , 33, D34-D38.
Genbank