[Genome] How can I get gene names out from positions of probes in a BED file?

[John Cumbers]

Hello,
I have drosophila affy tiled array data and two bed files.

I am having trouble pulling out gene names for the corresponding probes.
If I import the bed file as a custom track, then go to table browser and
click output at the bottom.  I've tried many of the settings, changing the
group from custom to all tables, but still I don't get any gene names, just
an output of position.   This maybe because no gene names are present in my
sample, (i.e. I'm just in intergenic regions) but I doubt it.  Am I doing
something wrong?  If it is because I don't have any genes there, then how
can I find which genes are nearest to these sites?

As a second question, do you know of a computational transcription factor
binding site predictor that outputs predicted binding sites as a bed file,
or similar file that can be intersected with the tiled array data above, to
test how good the predictions are?

Any help much appreciated,
John



-- 
John Cumbers,  Graduate Student
Biology and Medicine
Brown University, Box G-W
Providence, Rhode Island, 02912, USA
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