Thanks for reply. I am interested in finding the annotation of gene symbol on the Anopheles Gambaie Genome. Is there a table or annotation file from which I can somehow know the start and end position of a gene on this genome. There is a table named 'geneName.txt.gz' on http://hgdownload.cse.ucsc.edu/goldenPath/anoGam1/database/ and the entries are as follows
0 n/a 2299 1 thrB 10010 2 argA 8888 3 sam-pr 151442 4 hacA 9034 5 nifH 9589 6 azr 2487 7 LipL32 113812 The first column is ID, second is the geneSymbol and third is CRC. For other organisms there are Refseq files and from there I can get the coordinate information for gene symbols. But AnoGam1 does not have that file. Is there any other way to find BED files for these gene symbols or at least the start and end location of these genes. Thanks Fahim On Wed, Dec 7, 2011 at 2:13 PM, Vanessa Kirkup Swing <[email protected]>wrote: > Hi Fahim, > > We looked into your issue and we suspect that there is an issue with NCBI > and we suggest that you contact them. > > If you have further questions, please contact the mailing list: > [email protected]. > > Vanessa Kirkup Swing > UCSC Genome Bioinformatics Group > > ---------- Forwarded message ---------- > From: Fahim Mohammad <[email protected]> > Date: Tue, Dec 6, 2011 at 3:52 PM > Subject: [Genome] How the chromosomes with 2L and 2R are aligned > To: [email protected] > > > Hi > I am working on Anopheles Gambiae genome and I am facing problem when > comparing the result from NCBI and genome browser. > The chromosome names at UCSC browser that AnoGam1 have are chr 2L, 2R, 3L, > 3R, X and Un where as NCBI somehow combine L and R files together to get > one genome. > > Is there a way to make the data from UCSC and NCBI such that the chromosome > nomenclature as well as the coordinates becomes similar. > > Thanks > Fahim > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > > -- ------------------------------- Fahim Mohammad Bioinforformatics Lab University of Louisville Louisville, KY, USA Ph: +1-502-409-1167 web: http://bioinformatics.louisville.edu/lab/ ------------------------------- I think the reason people are dealing with science less well now than 50 years ago is that it has become so complicated. --James D. Watson<http://www.brainyquote.com/quotes/quotes/j/jamesdwat388959.html> _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
