How To Get Nssnps From Dbsnp For A Given Protein And Handle

Question

[Taqruibi]

Hi,

Is there a way to get the non-synonymous SNPs from dbSNP database for a given protein (NMXXXXX or NPXXXXX) and a particular submitter handle (e.g., CSHL)?

Thanks

Answer 1

[Pierre Lindenbaum]

You could use the following SQL query for the UCSC mysql server:

$ mysql  --user=genome --host=genome-mysql.cse.ucsc.edu -A   -D hg19

mysql> select G.name,S.name,S.chrom,S.chromStart,S.func,S.submitters
from snp132 as S,
refGene as G
where
S.submitters like "%CSHL%" and
G.name = "NM_001130924" and
G.chrom=S.chrom and
S.chromStart>=G.txStart and S.chromEnd<=G.txEnd and 
find_in_set(S.func,"missense")>0
;

+--------------+------------+-------+------------+----------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| name         | name       | chrom | chromStart | func     | submitters                                                                                                                                                              |
+--------------+------------+-------+------------+----------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| NM_001130924 | rs4926472  | chr1  |    9670833 | missense | 1000GENOMES,BCMHGSC_JDW,BCM_SSAHASNP,BGI,COMPLETE_GENOMICS,CORNELL,CSHL-HAPMAP,ENSEMBL,HGSV,HUMANGENOME_JCVI,ILLUMINA,KRIBB_YJKIM,PERLEGEN,SC_SNP,SSAHASNP,WI_SSAHASNP, |
| NM_001130924 | rs11799995 | chr1  |    9673045 | missense | 1000GENOMES,AFFY,CSHL-HAPMAP,ENSEMBL,ILLUMINA,ILLUMINA-UK,KRIBB_YJKIM,PERLEGEN,                                                                                         |
+--------------+------------+-------+------------+----------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
2 rows in set (40.89 sec)