Hi Vishnu, Please see my answers embedded below:
1. What is the easiest way to find genomic location of a SNP using rs number e.g. rs178810 on human genomic sequence on UCSC genome browser Type "rs178810" into the position search bar to get the genomic location of a SNP. 2. Which SNP database is used to find SNPs using the get DNA tool? The getDNA tool gets DNA from the reference genome, in this case hg19, not from the dbSNP database. 3. How often is this database updated? This data is updated whenever dbSNP releases a new set of SNPs. 4. Why does the SNPs search using Get DNA Tool at UCSC site produce different results when compared to NCBI dbSNP search? See my reply to #3. dbSNP and the getDNA tool should have show the same base in most cases, especially if the SNP only maps to one location. Is it possible that you are looking at snp132 on dbSNP and snp131 in the Genome Browser? We have not yet released snp132 but are hoping to release soon. I hope this information is helpful. Please feel free to contact the mail list again if you require further assistance. Best, Mary ------------------ Mary Goldman UCSC Bioinformatics Group On 2/15/11 3:27 PM, Mishra, Vishnu wrote: > Could you please let me know: > > 1. What is the easiest way to find genomic location of a SNP using rs > number e.g. rs178810 on human genomic sequence on UCSC genome browser > > 2. Which SNP database is used to find SNPs using the get DNA tool? > > 3. How often is this database updated? > > 4. Why does the SNPs search using Get DNA Tool at UCSC site produce > different results when compared to NCBI dbSNP search? > > Thanks > > Vishnu Mishra > Senior Scientist, Diagnostic Assay Development > Illumina, Inc. > 9885 Towne Centre Drive > San Diego, CA 92121 > Tel: 858-246-8813 > E-mail: [email protected]<mailto:[email protected]> > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
