Hi Donna, your discussion with Xianjun reminds me of requests from Zebrafish and Medaka genome browser users here that I repeatedly heard: Why are there so many self-chainable non-coding regions? I remember the "into the heart of darkness"-paper from Gill but he didn't really propose an explanation, as far as I remember. At 100-200 copies, the regions can hardly be repeats. Many of the examples I've been looking at are not conserved across species, so they don't look very "important" either. You told me that you increased your thresholds in the newer human assemblies to reduce the number of these features so I guess you don't consider them functional. But do you have any explanation for the many self-hits?
cheers Max On Thu, May 28, 2009 at 4:40 AM, Donna Karolchik <[email protected]> wrote: > hi Xianjun, > > You'll be pleased to hear that we do indeed have the zv8 assembly back > on our active project list, and hope to have it available on the public > site by perhaps sometime in July, depending on other incoming priorities > and staffing levels. We will announce the release on our > [email protected] mailing list when the browser becomes > available. > > -Donna > --------------- > Donna Karolchik > UCSC Genome Browser Project Manager > http://genome.ucsc.edu > > > Xianjun Dong wrote: >> Hi, >> >> OK. I am back with the same request now, after the assembly/annotation >> of Zv8 is done. >> >> We (and also the community, I think) know that, Zv8 was expected as a >> big improvement for Zv7, and it IS indeed, from the analysis report they >> released. So, we eagerly request UCSC, as one of the main hubs of >> data/tool for bioinformatics, to >> 1. update danRer6 (Zv8) new assembly on UCSC >> 2. make hg18:danRer6 chain/net alignment >> 3. put zebrafish self-chain alignment. >> >> Thanks >> >> Regards, >> >> Xianjun >> >> >> Jennifer Jackson wrote: >>> 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] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
