Hi Tlatmil, You should look at the Chain and Net tracks on mm9 and/or hg19. Also, take a look at these previous mailing list question: http://goo.gl/VoP6z. I think they might be helpful.
Please let us know if you have any additional questions: [email protected] - Greg Roe UCSC Genome Bioinformatics Group On 7/22/12 2:22 PM, Taltamil Tlatmil wrote: > Hi all, > > Maybe you can help me in this matter : > > I would like to find orthologous regions between genomic scaffolds and > complete genome (e.g., mm9/hg19). I understand this can be done with blastz > or lastz - which is the recommended one and can also do some chaining. I have > up to 30 processors available on Linux, but I'm not connected to any grid at > this point. I played a bit with lastz but I'm not getting biologically > reasonable mapping. Basically, I just need to find for each scaffold which > genomic region is its estimated ortholog, in order to map genes into the > scaffold and test their parallel synteny. > > Is it possible under this conditions to do that ? is there any > instuction/pipeline for that ? > > thanks > Tlatmil > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
