AutoSNPdb: an annotated single nucleotide polymorphism database for crop plants

被引：43

作者：

Duran, Chris ^{[1
]}

Appleby, Nikki ^{[1
]}

Clark, Terry ^{[1
]}

Wood, David ^{[1
,2
]}

Imelfort, Michael ^{[1
]}

Batley, Jacqueline ^{[1
,3
]}

Edwards, David ^{[1
]}

机构：

[1] Univ Queensland, Sch Land Crop & Food Sci, Australian Ctr Plant Funct Genom, Brisbane, Qld 4072, Australia

[2] Univ Queensland, Inst Mol Biosci, ARC Ctr Excellence Bioinformat, Queensland Facil Adv Bioinformat, Brisbane, Qld 4072, Australia

[3] Univ Queensland, ARC Ctr Excellence Integrat Legume Res, Brisbane, Qld 4072, Australia

来源：

NUCLEIC ACIDS RESEARCH | 2009年 / 37卷

基金：

澳大利亚研究理事会;

关键词：

SEQUENCE TAG DATA; DISCOVERY; TOOL;

D O I：

10.1093/nar/gkn650

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Single nucleotide polymorphisms ( SNPs) may be considered the ultimate genetic marker as they represent the finest resolution of a DNA sequence ( a single nucleotide), are generally abundant in populations and have a low mutation rate. Analysis of assembled EST sequence data provides a cost-effective means to identify large numbers of SNPs associated with functional genes. We have developed an integrated SNP discovery pipeline, which identifies SNPs from assembled EST sequences. The results are maintained in a custom relational database along with EST source and annotation information. The current database hosts data for the important crops rice, barley and Brassica. Users may rapidly identify polymorphic sequences of interest through BLAST sequence comparison, keyword searches of annotations derived from UniRef90 and GenBank comparisons, GO annotations or in genes corresponding to syntenic regions of reference genomes. In addition, SNPs between specific varieties may be identified for targeted mapping and association studies. SNPs are viewed using a user-friendly graphical interface. The database is freely accessible at http://autosnpdb.qfab.org.au/.

引用

页码：D951 / D953

页数：3

共 8 条

[1] BASIC LOCAL ALIGNMENT SEARCH TOOL [J].