---------- Forwarded message ---------- From: Ao Zhou <[email protected]> Date: 2010/8/24 Subject: Re: [Genome] About: Getting homolog regions in Rat, with Mouse genomic coordinates To: Mary Goldman <[email protected]>
Update: Liftover works, thank you very much!!! :) I thought it could only be used in version transforms~ I does work between mouse and rat! There is another question, in this page: http://genome.ucsc.edu/cgi-bin/hgTracks?org=Mouse&db=mm8&position=chr1:175561150-175578575 I think the level 1 net alignment should have the most sequences mapped right? But in this page it seems like a big gap... what is the reason please? Thank you :) 2010/8/24 Ao Zhou <[email protected]> Dear Mary, > > Thank you so much for answering my questions! > > For the first tool LiftOver, this is helpful in transforming the MM8 > coordinates to MM9 coordinates, > but cannot help in the homolog region search between Mouse and Rat. > > For the second tool, actually the regions I'm looking for are all > inter-genic regions (we are looking for unknown genes), > so it may not work either... T_T > > So is there any possible methods to get the results? > What I wanted to do is: Given a mouse region, then search for the rat > region with the highest alignment score to the mouse region. > Thank you! :) > > > > > 2010/8/24 Mary Goldman <[email protected]> > > 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! >>> >>> >>> >> > > > -- > Ao Zhou > Ph.D. Student, > Bioinformatics Program, > School of Informatics, IUPUI > Tel: 317-372-7004 > -- Ao Zhou Ph.D. Student, Bioinformatics Program, School of Informatics, IUPUI Tel: 317-372-7004 -- Ao Zhou Ph.D. Student, Bioinformatics Program, School of Informatics, IUPUI Tel: 317-372-7004 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
