Table 2 Related online tools for genome analysis.

 Database of Transcriptional Start Sites (DBTSS)

Suzuki, Y., Yamashita, R., Sugano, S. & Nakai, K.

http://dbtss.hgc.jp/index.html

 The Eukaryotic Promoter Database (EPD)

Schmid, C.D., Praz, V., Delorenzi, M., Perier, R. & Bucher, P.

http://www.epd.isb-sib.ch/index.html

 Human Promoter Database (HPD)

Davuluri, R.V., Suzuki, Y., Sugano, S. & Zhang, M.Q.

http://zlab.bu.edu/~mfrith/HPD.html

 Databases of Orthologous Promoters (DoOP).

Barta, E. et al.

http://doop.abc.hu/

 Multiple Em for Motif Elicitation (MEME)

Bailey, T., Elkan, C., Grundy, B. & Gribskov, M.

http://meme.sdsc.edu/meme/website/meme.html

 The Gibbs Motif Sampler

Thompson, W., Rouchka, E.C. & Lawrence, C.E.

http://bayesweb.wadsworth.org/gibbs/gibbs.html

 Possum

Fu, Y., Frith, M.C., Haverty, P.M. & Weng, Z.

http://zlab.bu.edu/~mfrith/possum/

 UCSC Browser

Karolchik, D. et al.

http://genome.ucsc.edu/cgi-bin/hgGateway

 VISTA Browser

Frazer, K.A., Pachter, L., Poliakov, A., Rubin, E.M. & Dubchak, I.

http://genome.lbl.gov/vista/index.shtml

 The GRID

Tyers, M., Breitkreutz, B., Jorgensen, P. & Breitkreutz, A.

http://biodata.mshri.on.ca/grid/servlet/Index

 Drosophila Developmental Gene Expression Timecourse

Stolc, V. et al.

http://genome.med.yale.edu/Lifecycle/

 Patterns of gene expression in Drosophila embryogenesis

Tomancak, P. et al.

http://www.fruitfly.org/cgi-bin/ex/insitu.pl

 Toucan 2

Aerts, S. et al.

http://www.esat.kuleuven.ac.be/~saerts/software/toucan.php#tut

 CREME

Sharan, R., Ben-Hur, A., Loots, G.G. & Ovcharenko, I.

http://creme.dcode.org/

 Cluster-Trainer

Frith, M. & Weng, Z.

http://zlab.bu.edu/cluster-buster/ctrain.html

 Co-Bind

GuhaThakurta, D. & Stormo, G.D.

http://ural.wustl.edu/~dg/co-bind.html

 Mtf-dist

Papatsenko, D.

http://webdisk.berkeley.edu/~dap5/data_01/tools.html

 ModelInspector (Genomatix)

Frech, K., Danescu-Mayer, J. & Werner, T.

http://www.genomatix.de/products/index.html