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On Thursday 04 January 2007 09:34, Romain Desprat wrote: > Dear bioconductor List, > > I have a file with the name of my probes, the start and end position, > sequence... and I want to know if this probes is in Exon, intron and to > get genomic features automatically.The goal would be to get all these > results in one table.For one probe I can do it myself on USCS, but I want > to do it for the 300 000 probes of my tiling array (nimblegen). > Is there any package that could help me or does anyone did solve this issue > ? This is pretty simple to do via the UCSC table browser. In brief, make your probes into a custom track. Then ask for the overlap of your probes with exons, etc., in the Table Browser. For more detailed instructions, there is a link on the UCSC pages to contact them. Just copy your email to them and they will likely give you step-by-step instructions on how to do what you are asking within a few hours; they are quite helpful in general. An alternative is to use the Galaxy server here (which seems to be down at this moment): http://g2.bx.psu.edu/ Hope this helps. Sean