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
