Single nucleotide polymorphism databases

This list was assembled using NCBI Entrez SNP, dbSNP BUILD 128. Abbreviations dbSNP rs No, single nucleotide polymorphism database reference cluster number ADRB2, beta-2-adrenergic receptor, surface. 

Single Nucleotide Polymorphism Database (dbSNP) of Nucleotide Sequence Variation. URL http //www.ncbi.nlm. nih.gov/SNP/index.html. Uses SNP in the much looser sense of minor genetic variations and includes microsatellite repeats and small insertion/deletion polymorphisms. 

Single Nucleotide Polymorphism Database (dbSNP) www.ncbi.nhn.iuh.gov/entrez query.fcgi db=snp (National Center for Biotechnology Information, NCBI) SNP... 

Keywords Bioinformatics database disease dmg function genotype interaction pathway pharmacogenomics phenotype single-nucleotide polymorphism (SNP) software stmcture systems biology. 

Click on the link indicated by H next to the Nucleotide-nucleotide BLAST (blastn) to access the problem. This problem describes how to obtain single-nucleotide polymorphism (SNP) information in similar sequences in the database. Hermankova et al. (8) studied the HIV-1 drug resistance profiles in children and adults receiving combination drug therapy. To identify the SNPs in the HIV-1 isolates from these patients, or other similar sequences in the database, use the sequence from one of the patients given next and run a nucleotide-nucleotide BLAST search as described in the problem previously listed. Format the results using the Flat Query with Identities option from the Alignment View pull down menu under the Format options (see Note 3). 

Fig. 3. Query-anchored alignment view for finding single-nucleotide polymorphism (SNP) from the nucleotide-nucleotide search problem 2. Nucleotides in the database sequences identical to the query HIV-1 sequence are indicated by dots and SNPs are indicated by the one letter nucleotide code. The A/G SNP at the query nucleotide 10 is highlighted.

Single-nucleotide polymorphisms (SNP) presentation. FOOTER has recently made available a function that will allow the identification and presentation of known SNPs in the examined promoters. The SNPs are derived from the dbSNP database (12). Though the presence or absence of SNPs in the promoter region(s) does not weight into the FOOTER analysis, it can provide useful information to the user about possible sites that could be affected by a polymorphism. 

JSNP—A Database of Japanese Single Nucleotide Polymorphisms... 

Sherry, S. T, Ward, M., and Sirotkin, K. (1999). dbSNP-database for single nucleotide polymorphisms and other classes of minor genetic variation. Genome Res 9 677-679. 

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