Hi Ao, There two other tools that may be able to help you. The first is the liftOver tool (http://genome.ucsc.edu/cgi-bin/hgLiftOver), which allows you to lift batch coordinates between assemblies. I am not sure if this will work for you, given that it uses the same tables you were accessing in your first method, but it is probably worth a try.
The other tool that may be able to help you is the rnBlastTab table. This table was built by taking all the genes in UCSC Genes, blasting them against the rat genome and then filtering out the non-sytenic hits. However, this table is only helpful if your all your genomic regions are genes in the UCSC Genes track. If this is so, please write back and I will email further instructions on how to use this table. I hope this information is helpful. Please feel free to contact the mail list again if you require further assistance. Best, Mary ------------------ Mary Goldman UCSC Bioinformatics Group On 8/22/10 10:47 AM, Ao Zhou wrote: > Hi, there, > > I'm a beginner in UCSC genome browser, and I'm attempting to find out > Rat homolog regions with Mouse genomic coordinates. > The query composites of thousands tuples like this, the db version is *mm8*: > chrX 138292125 138297400 > > What I want is like this, the db version is Rat* Rn4*: > chrX - 35494226 35500120 > > I've already tried two methods, but both of them are not perfect: > > 1. In the table browser, Mammal -> Mouse -> Comparative Genomice -> Rat/Net > -> input coordinate restrictions > Pros: Batch download is available in this method > Cons: The derived regions are actually highly homolog sub-regions within > the query Mouse region, > however, what I need is a single Rat region that can be > considered as a homolog gene to the query Mouse region. > 2. In the genome browser, Comparative Genomics -> Rat Full -> Click on the > net alignment -> See the alignments > Pros: The two regions are mapped, and a side by side alignment is also > shown. > Though the Rat coordinates are not clearly displayed, it can be > infered from the alignments. > Cons: Batch download is not available, I have thousands of Mouse regions > to query... > > Other methods: > I'm also thinking of do the mapping manually, or use PHP to search the > result pages of the side by side alignment. > But before doing that I have to make sure there's not an efficient way > to do this task~ > > Could anyone tell me what tool I should use please...? > Thank you! > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
