Hi, I am curious how UCSC website locate the position (in species B) corresponding to the part of chain that is in a window (in species A).
To explain my question clearly, I have an example here. For instance, if you open the zebrafish chain alignment track in the following human locus page: http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18&position=chr11:31787916-31796585 You can see there are two chains under the region. Clicking one of them, we will see another page: http://genome.ucsc.edu/cgi-bin/hgc?hgsid=134848741&o=31083313&t=33335216&g=chainDanRer5&i=124&c=chr11&l=31787915&r=31796585&db=hg18&pix=900 On this page, there is a link for "Open Zebrafish browser <http://genome.ucsc.edu/cgi-bin/hgTracks?db=danRer5&ct=&position=chr25%3A15181364-15184384> at position corresponding to the part of chain that is in this window." Clicking that will exactly bring us to the zebrafish region(chr25:15181364-15184384), which is exactly the region I am interested to get by script. It seems that you have the trick to cut the chain accurately. OK, my question is: how do you make this done so exactly and so quickly? Esp. when there are double lines at the end of the query region, which represent more complex gaps involving substantial sequence in both species. This might be answered simply by "UCSC are using a super power server....and well-structured databases". Well, I guess this might be one of the main reasons. But, beside that, I am curious UCSC must be using some tricky way to get it quickly. I've looked into the Chain (and chainLink) table. Only alignable blocks are stored there, which means it's no problem to get the corresponding position if the start/end position of the query reside inside the blocks. But how about if it resides in the complex gap (double line in the chain track)? How can you know exactly where its corresponding position in zebrafish, for example? Can I know the script, or the way how you make it? Hope I explain my question clearly Thanks -- ========================================== Xianjun Dong PhD student, Lenhard group Computational Biology Unit Bergen Center for Computational Science University of Bergen Hoyteknologisenteret, Thormohlensgate 55 N-5008 Bergen, Norway E-mail: [email protected] Tel.: +47 555 84022 Fax : +47 555 84295 ========================================== _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
