Since
Oct.09.2002
Last update
Sep.22.2008
Version 15.1
Now in this DB
13909 STSs
10848 SNPs
Map information
NCBI Build 36
rsSNP information
dbSNP Build 128
Update history
|
|
|
|
We newly developed a Windows software called "QSNPlite" that comprehensively interprets the data of SSCP and sequencing analyses obtained from capillary array electrophoresis systems used in the quantitative characterization of SNPs. The package is now available for those who have contacted us ( ).
|
|
|
|
|
| |
Single nucleotide polymorphisms (SNPs) are bi-allelic genetic markers abundantly distributed throughout human genome. SNPs in the transcriptional promoter regions are the candidates of the cis-acting determinant for the inherited variations in gene expression among individuals. Cataloguing of these SNPs should be useful in the study to find relation of regulatory mechanisms of genes with medical importance, such as those conveying disease resistance or affecting drug metabolism. This database accumulates and presents experimental data of sequences and allele frequencies of SNPs in the promoter regions. The regions studied here were mainly 1.0 kb upstream and 0.2 kb downstream of transcriptional start regions (TSS), which have been defined as the 5' end of full length cDNA, obtained from the database of transcription start sites (DBTSS: http://dbtss.hgc.jp).
SNP genotyping/ quantification is based on SSCP analysis using capillary electrophoresis that has been established by us (Orita et al., 1989; Inazuka et al., 1997; Hayashi et al., 2001; Tahira et al., 2002; Kukita et al., 2002; Baba et al., 2003). In this method, alleles are separated into peaks, and their frequencies can be reliably and accurately quantified from their peak heights of pooled DNA (Sasaki et al., 2001). The raw data of SSCP analysis obtained from various capillary-array apparatuses were interpreted by a newly developed fragment analysis software, "QUISCA" (Higasa et al., 2002).
To manage SSCP and sequencing analyses for discovering SNPs and determining their allele frequency at a large scale, we have developed a relational database, "dbQSNP Conductor", that runs on postgreSQL, and supports designing experiments, analyzing results of SSCP/sequencing from various capillary-array DNA sequencers, and verifying these results to minimize error (Tahira et al., 2005). This site, "dbQSNP Public", is a repository of STS/SNP information obtained by "dbQSNP conductor". SSCP and sequence trace data are just a few clicks away, and thus, integrity of the data can be confirmed.
|
|
|
|
|
| |
You can search dbQSNP records by Blast-search against STS sequences in this database, by key word or by chromosomal location.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Data of dbQSNP is downloadable as two kinds of files. Sequences of SNPs and its flanks are provided in fasta format whereas the allele frequencies are in tab-delimited format.
In addition, we begin to provide our data in PML (Polymorphism Markup Language) which is based on XML, to facilitate portability of our data on SNPs and other sequence variations.
The files are available at the download page.
|
|
|
|
