Hello Fahim, Unfortunately we do not have a single table for A. gambiae that contains both gene symbols such as these as well as transcription or coding start/end coordinates. For gene coordinates we recommend using the table associated with the Ensembl track for this assembly. You can download this table by going to the Table Browser (http://genome.ucsc.edu/cgi-bin/hgTables) and select:
group: Genes and Gene Prediction Tracks track: Ensembl Genes table: ensGene region: genome output format: selected fields from primary and related tables the click "get output" this will take you to a menu where you can select which columns of information you want to appear in your output. We unfortunately do not have a table for converting Ensembl IDs in A. gambiae to the types of identifiers you list, you may be able to find such a resource on the Ensembl site. You can read more about the Ensembl data set on its description page - accessible by clicking on the gray bar to the left of the track in the main display or on the track title above the pulldown menu for the track in the browser. Best regards, Pauline Fujita UCSC Genome Bioinformatics Group http://genome.ucsc.edu On 12/7/11 1:06 PM, Fahim Mohammad wrote: > 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 >> >> > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
