Hello Nicholas, You are correct, the alignments are with respect to the Drosophila Melanogaster genome. If a region is included only partially in the MAF, you can try to see where else in the MAF the surrounding regions map using the dm chain/net tracks back in the target genome. You can also just go to that region in the target genome and open a Gene track and examine what is annotated there. As you probably know, it turns out that flies are a bit more different from each other than one might initially expect.
If you do find MAF blocks that you want to "stick together" - the data can be saved in a custom track using the Table browser and sent over to Galaxy. Many tools to manipulate MAF data are available there. You maybe be able to develop a workflow for your analysis using their tools. Best wishes, Jennifer --------------------------------- Jennifer Jackson UCSC Genome Bioinformatics Group http://genome.ucsc.edu/ On 2/11/10 4:22 PM, Nicholas Price wrote: > Hi > > I have the coordinates for some Drosophila Melanogaster microRna genes and I > am trying to find the othologs in the the other 14 insect genomes that you > have..So I am basically using multiz15 of your table browser..My question is > when the alignment returned is in blocks and I have to concatenate them, am > I missing any internal sequence information from the other species > sequences.. > > That is when you query the db using the melanogaster region, it will return > all blocks that overlap that region, cropped to that region;While this > should return the orthologs in each species, it is not guarenteed to return > complete orthologs > > Nicholas > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
