To those who might concern, Zebrafish has been one of the most studied models in study of whole genome duplication and development, but its genome assembly is not so well (which is naturally difficult also due to the whole genome duplication there). We also noticed much duplication closely mapped in same chromosome, which actually are proved as assembly error in zv7, by BLATing in the new assembly Zv8 (http://pre.ensembl.org/Danio_rerio/Info/Index). Before Zv8 annotation get done (which might help to some extent, but not all), I am thinking if UCSC could make a self-chain for zebrafish, just like you did for human. If that information offered, we could write a script to quickly check those 'tandem' duplications close in genome, which can eventually help to improve the quality of the current assembly.
If you think this might not be done in the coming soon by your plan, I will be appreciated if you can offer any assistance for me to try it myself. Regards, -- Sterding (Xianjun) Dong PhD student, Boris Lenhard's group Bergen Center of Computational Science Bergen University, Norway Mobile: 0047-47361688 Telephone: 0047-55584022 Skype: xianjun.dong _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
