Hello, The comparisons from one version of the genome to another is done using a program called BlastZ. The complete methods are the same as for a "Chain" track in the "Comparative Genomics" track grouping. To view this, open up the UCSC Browser, click into Genomes, select any cow assembly and sumit. Scroll down to the track group, open it up, and click on one of the "XXX Chain" track names.
Lifting an entire chromosome may be tricky. It is likely that the largest lifted pieces back to the same chromosome are accurate and the smaller pieces lifted to different chromosomes were part of the correction made by the scientists who are finishing the genome. Your method probably works fine (using Galaxy) but there is no reason to use an external tool. In fact, the parameters may require some tuning to limit the results in Galaxy (and in UCSC's Utilities->Batch Coordinate Conversion(hgLiftOver)). Instead, using the UCSC Browser's Convert tool is an easy way to use the liftOver tool in the Browser and interpret results. If you are curious about a region, just click on it and open the browser window to view annotation features. Starting with: Cow Aug. 2006 (bosTau3) - chr13:1-83,371,483 1) Open the starting species' browser and put in the coordinates and submit. 2) Click on "Convert" in the top blue bar. Select New genome=Cow, New assembly=Oct.2007 and submit. Results: The top hit, chr13:44618-82887899 (61.8% of bases, 98.4% of span), is the best match. The rest are smaller fragments and rearrangements, likely part of the reassembly process. Native repeats are carefully handled and should not be a major factor. There is also themethod, but it is more complicated and will fail on such large regions without some parameter tuning. Good luck and please let us know if you have additional questions, Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Team Alpha" <[email protected]> wrote: > From: "Team Alpha" <[email protected]> > To: "Jennifer Jackson" <[email protected]> > Sent: Monday, August 3, 2009 9:25:42 AM GMT -08:00 US/Canada Pacific > Subject: Re: [Genome] Question about ucsc browser? > > Hi Ms. Jackson, Our group has a quick question. Our summer project > team is trying to figure out where chromosome 13 is located on Cow on > aug 2006 and in Cow Oct. 2007. We are using the galaxy liftover > interface to see exactly where it is located on the new version of the > chromosome. But when we do this we keep getting a range of positions. > Our Group was wondering if you have to use ncbi blast program to get > the position. > > > These are the parameters we are putting into the UCSC table browser. > clade: Mammal > Genome: Cow > Assembly: Aug. 2006 > Group: All Tables > Database: bosTau3 > Region: position (Chr13 :46,694,506-46,694,506 ) > output format BED - browser extensible data > > > We are trying to understand more about how the chr changes position > from one version to another. > thank you for your help > > On Tue, Jul 28, 2009 at 5:57 PM, Jennifer Jackson < [email protected] > > wrote: > > > Hello, > > For the position search, I was unable to duplicate your result. In the > main browser or table browser, format the location as specified and > submit. Even just using a single position instead of a range is OK. > Ex: chr13:46,694,506 is translated to chr13:46,694,506-46,694,506. In > the Assembly browser, use the top link "DNA" for fasta sequence. For > BED format from tracks, use the Table browser. > > The chain and net process is explained in detail on those track's > description pages. To view, bring up the track in the Table browser > and click through to the primary table to view schema, linked tables, > and description/methods. Or, using the Assembly browser, click on the > track name, the description methods starts after the top header info > (which also has a link to the primary table). > > We hope this helps, > Jen > > > ------------------------------------------------ > Jennifer Jackson > UCSC Genome Bioinformatics Group > > ----- "Team Alpha" < [email protected] > wrote: > > > From: "Team Alpha" < [email protected] > > > To: [email protected] > > Sent: Tuesday, July 28, 2009 12:23:41 AM GMT -08:00 US/Canada > Pacific > > Subject: [Genome] Question about ucsc browser? > > > > > > > Hi, I had a few question about the UCSC browser. On the browser I > was > > trying > > to find a single position in chr 13, Like chr 13 at position > 46694506. > > But I > > have not been able to just get that position and save it to a bed > > file. > > The next question was about the over.chain file. I have been reading > > that > > this file was or is created by a process called comparative chain > > process. > > Is there any way I can learn more about the creation of a over.chain > > file? I > > was wonder how this files is created to compare to version of the > > same > > species or even understand how this works cross species. Any > > documentation > > would be greatly appreciated. > > > > Thanks for any help you can give. > > _______________________________________________ > > Genome maillist - [email protected] > > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
