Hello Zhidong, Your conclusion sounds right to me, but the data you are referring to is not from UCSC, and we do not host it in our panda browser. I recommend contacting BGI directly about their data if you have questions.
-- Brooke Rhead UCSC Genome Bioinformatics Group ----- "zhidong yuan" <[email protected]> wrote: > Dear Vanessa, > > Thank you for your reply. > > As scaffold1006 is coresponding to GL193131.1 in > localID2acc<ftp://ftp.ncbi.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Ailuropoda_melanoleuca/AilMel_1.0/Primary_Assembly/localID2acc>, > and > "scaffold1006 EP3 promoter 58200 58600 > 0.39661930963539976 > . . ID=Promoter00191;" is in > ftp://public.genomics.org.cn/BGI/panda/genome_annotation/regulatory/panda.scafSeq.gapFilled.noMito.fa.masked.ep3.promoter.join.gff.gz > > Could I think that is equal to > GL193131.1 EP3 promoter 58200 58600 > 0.39661930963539976 > . . ID=Promoter00191 > for only the scaffold numbers changed but their sequences are equal. > Is it > all right? > > Best wishes, > > Zhidong > > > > 2010/8/5 Vanessa Kirkup Swing <[email protected]> > > > Dear Zhidong, > > > > The data for this assembly was obtained from NCBI and we were able > to > > locate this page for you to use: > > > > > > > ftp://ftp.ncbi.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Ailuropoda_melanoleuca/AilMel_1.0/Primary_Assembly/localID2acc > > > > Hope this helps! Please don't hesitate contacting the mailing list > if you > > have further questions. > > > > Vanessa Kirkup Swing > > UCSC Genome Bioinformatics Group > > > > ----- Original Message ----- > > From: "zhidong yuan" <[email protected]> > > To: [email protected] > > Sent: Tuesday, August 3, 2010 7:36:05 AM GMT -08:00 US/Canada > Pacific > > Subject: [Genome] How could I map the annotation provided in panda > database > > to UCSC genome browser? > > > > Hi, could someone tell me how to find the corresponding scaffold in > UCSC > > Genome Browser to the one provided in the Giant Panda Database ( > > > http://panda.genomics.org.cn/page/panda/index.jsp)<http://panda.genomics.org.cn/page/panda/index.jsp%29>.? > > For instance, > > scaffold1020 corresponding which GL? in the UCSC Genome Browser? How > could > > I > > map the gene annotation, regulate elements and ncRNA gene in panda > database > > to the UCSC Genome Browser for some they only provide genome > coordinate? > > > > Thank you. > > > > -- > > Zhidong > > _______________________________________________ > > Genome maillist - [email protected] > > https://lists.soe.ucsc.edu/mailman/listinfo/genome > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
