To your answer # 2 below, Get DNA Tool has the option to get DNA sequence as well as SNPs (extended case/color option) flagged on the retrieved sequence. The question I had was with regard to the SNP database used when using get DNA tool and choosing the snp option also. It appears from your responses that UCSC browser also uses dbSNP database but is probably a release behind NCBI. Is that correct?
Thanks vish -----Original Message----- From: Mary Goldman [mailto:[email protected]]<mailto:[mailto:[email protected]]> Sent: Wednesday, February 16, 2011 1:33 PM To: Mishra, Vishnu Cc: [email protected]<mailto:[email protected]> Subject: Re: [Genome] SNP search 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]<mailto:[email protected]%3cmailto:[email protected]>> > > _______________________________________________ > Genome maillist - [email protected]<mailto:[email protected]> > https://lists.soe.ucsc.edu/mailman/listinfo/genome 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
