Hi Yuan, The Conservation track in hg18 has control options that would allow you to remove any species not in your set. This is a compound track - meaning that conserved regions are a part of the sub-track set. Download/data access info & options: http://genome-test.cse.ucsc.edu/FAQ/FAQdownloads#download1 http://genome-test.cse.ucsc.edu/FAQ/FAQdownloads#download29 http://genome-test.cse.ucsc.edu/FAQ/FAQtracks#tracks21
If you still want to do this on your own, the Conservation track is still a good reference. For each species, the methods we used are outlined. Different alignment methods were used for different species based on biological reasoning (evolutionary distance, quality of genomic, etc). For details about each pair-wise, see the individual tracks in that species' genome browser and review the creation methods. Some of these may not be on the public server, but on the test server at http://genome-test.cse.ucsc.edu/. Please note that all tracks on the test server /that are not/ on the regular public server have not undergone formal QA and may have sparse methods - although you should be able to identify similar tracks on the public server (in another species) with complete methods listed. However - with your list of genomes - this should not be a problem. Some notes from a UCSC Scientist that creates this type of data: > http://genomewiki.ucsc.edu/index.php/Whole_genome_alignment_howto > > That is a great write-up by a power-user who managed to sort of > duplicate our process locally, for a small genome. > > And we should also stress upfront that the process requires big > compute resources. If they're working with vertebrate genomes, they > should have access to a cluster with at least ~50 CPUs (more is > better) and if mammalian genomes, at least a few hundred CPUs. > Otherwise the compute time is prohibitive. > > And we should probably tell them that we now use lastz, a greatly > improved replacement for blastz. > > http://www.bx.psu.edu/miller_lab/dist/README.lastz-1.01.50/README.lastz-1.01.50.html > > Angie > Thanks, Jennifer Jackson UCSC Genome Bioinformatics Group Yuan Hao wrote: > Dear List, > > I would like to create my own multiple alignment file for hg18, mm9, > rn4 and canFam2 from UCSC pairwise alignments by using Multiz/TBA > aligner. I got following several questions which I am not sure yet > after a broad reading. It would be very appreciated if you could shed > some lights on them: > > - Which aligner, Multiz or TBA, would be better if my purpose is to > study the motif conservation on the final MAF. > > - Multiz/TBA takes pairwise alignment in .maf format. While from UCSC > I can only find pairwise alignment in .chain, .net or axtNet format. I > found there are programs available in Kent source to do the format > convert: chainToAxt, netToAxt or axtToMaf. My question is which > pairwise format should I download to create multiple alignment? > > - Is there anything else I missed here during this process? > > Thank you very much in advance! > > Kind regards, > Yuan > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
