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Do you use?

the Gibbs sampler for DNA the Gibbs sampler for proteins both

What type of experimental data do you most often submit to the Gibbs web site?

phylogenetic sequence data  (the promoter regions upstream of a single orthologous gene from several species)
co-expression data from microarray experiments (from a single species, the promoter regions of genes that were co-expressed)
expression data from promoter fusion experiments
transcription factor binding assays (the promoter regions that are bound by a protein in experiments such as gel-shift, DNaseI, ChIP)
protein data
other

What type of species data do you most often submit for Gibbs sampling?

bacterial DNA sequences
yeast/fungal DNA sequences
Drosophila DNA sequences
C.elegans DNA sequences
mammalian DNA sequences
other

The web page currently has prokaryotic and eukaryotic default settings.  Do you use these

yes
no
sometimes

What type of motif are you typically interested in looking for?

transcription factor binding sites
sigma factor / RNA polymerase binding sites
splice sites
repeat sequences
protein motifs
signal peptides
transmembrane segments
other

Do you typically search for

one motif
multiple motifs simultaneously

Do you typically expect that there will be

a single site per sequence for a motif
multiple sites per sequence for a motif
usually don't know

How many fasta sequences do you typically input to the Gibbs sampler?

1-10 11 - 50  51 - 100  101 - 500  > 500

Roughly how much total sequence data does this typically represent?

< 100 bp 100 - 1,000 bp 1,000 - 10,000 bp 10,000 - 100,000 bp > 100,000 bp

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