Upstream Sequence Data			Binding Site Data
Enter FASTA formated DNA sequences			Select Organism (all sites are from the TRANSFAC public release version 6.0 unless otherwise stated)	yeast, TRANSFAC sites (S.c.) yeast, SCPD mapped sites yeast, SCPD consensus sequences Agrobacterium tumefaciens Aspergillus nidulans, Emericella nidulans cattle, Bos taurus chick, Gallus gallus clawed frog, Xenopus clawed frog, Xenopus laevis domestic pig, Sus scrofa duck, Cairina moschata fission yeast, Schizosaccharomyces pombe flesh fly, Sarcophaga peregrina french bean, Phaseolus vulgaris fruit fly, Drosophila melanogaster fruit fly, Drosophila orena fruit fly, Drosophila virilis garden snapdragon, Antirrhinum majus hamster hamster, Cricetulus griseus human, Homo sapiens maize, Zea mays mouse, Mus domesticus mouse, Mus hortulans mouse, Mus musculus Neurospora crassa oat, Avena sativa L. vc. Gary pea, Pisum sativum Petunia sp. potato, Solanum tuberosum quail, Coturnix coturnix rabbit, Oryctolagus cuniculus rainbow trout, Salmo gairdneri rat, Rattus norvegicus rat, Rattus rattus rice, Oryza sativa sea urchin sea urchin, Lytechinus pictus sea urchin, Paracentrotus lividus sea urchin, Pseudocentrotus miliaris sea urchin, Strongylocentrotus purpuratus sheep, Ovis aries silk moth, Bombyx mori slime mould, Dictyostelium discoideum soybean, Glycine max soybean, Glycine max cv. Provar tobacco, Nicotiana tabacum tomato, Lycopersicon esculentum wheat, Triticum aestivum yeast, Candida glabrata yeast, Kluyveromyces lactis yeast, Yarrowia lipolytica
			or organism group	yeasts plants viruses animals insects
Enter list of systematic ORF names (Saccharomyces cerevisiae ORFs only)			or enter TF binding sites (FASTA format)
Further Options Thresholds Select GC content (for background probability) 0% 5% 10% 15% 20% 25% 30% 35% 40% 45% 50% 55% 60% 65% 70% 75% 80% 85% 90% 95% 100% Minimum number of occurences Automatically determine GC content from input sequence? Yes : No : Expectation value Combine user defined and TRANSFAC sites? Yes : No : Minimum expectation ratio Colour scheme? random fixed

Paul Boardman (peb@bms.umist.ac.uk) Department of Biomolecular Sciences, UMIST, P.O. Box 88, Manchester M60 1QD UK

SiteSeer: visualisation and analysis of transcription factor binding sites in nucleotide sequences. Nucleic Acids Res. 2003 Jul 1;31(13):3572-5.