Hello, One of our scientists has some specific ideas concerning the zebrafish assembly as follows:
They think the main reason the genome is so difficult to assemble was due to the DNA collection strategy:- http://www.sanger.ac.uk/Projects/D_rerio/Zv3_assembly_information.shtml The FAQ indicates there should be a finished genome by the end of this year: http://www.sanger.ac.uk/Projects/D_rerio/faqs.shtml#factsnine Maybe you could discuss your suggestion with the sequencing project, and if it would help them, we could discuss it further. Thank you for your offer to help improve the data, Jennifer Jackson UCSC Genome Bioinformatics Group Xianjun Dong wrote: > 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, > > _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
