Hello Mary, members of the list: Well, I would like to do some alignments on the different promoters of different species. I am running a phylogenetic foot-printing technique and I want to have as many genes from different species as possible.
>From what I could gather from the mailing list, xenoRefFlat consists of other genes from other species aligned into the organism. This would give me a larger list of genes because some organisms only have 1000+ gene annotations in refFlat. Do you think using xenoRefFlat for this purpose makes sense? Regards, Arnoldo Muller On Tue, 2010-10-05 at 15:51 -0700, Mary Goldman wrote: > Hi Arnoldo, > > The answer to your question depends on what you are going to use the data > for. Please keep in mind that the UCSC Genome Browser simply displays data; > it does not say what is or is not acceptable analysis of this data. > > Please feel free to contact the mail list again if you require further > assistance. > > Best, > Mary > ------------------ > Mary Goldman > UCSC Bioinformatics Group > > ----- Original Message ----- > From: "Arnoldo Jose Muller-Molina" <[email protected]> > To: [email protected] > Sent: Tuesday, October 5, 2010 1:31:56 PM GMT -08:00 US/Canada Pacific > Subject: [Genome] About xenorefflat > > Hello! > > I would like to extract promoter regions of various sizes from different > vertebrates. I am aware that you provide the upstreamXXXX.fa.gz files > but I would like to have them repeatmasked. > > I decided to extract my data directly from the chromosomes using > refFlat.txt files. I have noticed that some organisms have a small > number of entries. Some organisms like the Panda do not have refFlat.txt > at all. Would it be safe to approximate promoter regions with > xenoRefFlat? > > Regards, > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
