A pipeline for high throughput detection and mapping of SNPs from EST databases.
A pipeline for high throughput detection and mapping of SNPs from EST databases.
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DOI：
10.1007/s11032-009-9377-5
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发表时间：
2010-06
期刊：
影响因子：
--
通讯作者：
van der Linden CG
中科院分区：
文献类型：
--
作者：
Anithakumari AM;Tang J;van Eck HJ;Visser RG;Leunissen JA;Vosman B;van der Linden CG
单核苷酸多态(SNPs)代表了可用作分子标记的最丰富的遗传变异类型。隐藏在序列数据库中的SNP可以使用生物信息学工具解锁。为了有效地应用这些SNP，序列集应该尽可能没有错误，针对单个基因座，并适合所选择的SNP评分平台。我们利用QualitySNP软件开发了一条从有或没有质量信息的公共EST数据库中有效地挖掘SNP的流水线，选择了可靠的SNP，并准备了在Illumina GoldenGate基因分型平台上进行分析的座位。利用公开的马铃薯EST数据，对两个二倍体作图群体的个体进行基因分型，然后在两个群体中定位SNP标记(可能的基因)，证明了该管道的适用性。超过7000个可靠的SNP被鉴定出来，它们符合金门平台上的基因分型标准。在SNP阵列上的384个SNP中，大约12%的SNP退出了。对于两个马铃薯作图群体165和185个SNP，分离的SNP座位可以被定位在各自的遗传图谱上，这说明了我们的SNP选择和验证工作的有效性。本文的在线版本(doi：10.1007/s110320099377-5)包含补充材料，授权用户可以使用。
Single nucleotide polymorphisms (SNPs) represent the most abundant type of genetic variation that can be used as molecular markers. The SNPs that are hidden in sequence databases can be unlocked using bioinformatic tools. For efficient application of these SNPs, the sequence set should be error-free as much as possible, targeting single loci and suitable for the SNP scoring platform of choice. We have developed a pipeline to effectively mine SNPs from public EST databases with or without quality information using QualitySNP software, select reliable SNP and prepare the loci for analysis on the Illumina GoldenGate genotyping platform. The applicability of the pipeline was demonstrated using publicly available potato EST data, genotyping individuals from two diploid mapping populations and subsequently mapping the SNP markers (putative genes) in both populations. Over 7000 reliable SNPs were identified that met the criteria for genotyping on the GoldenGate platform. Of the 384 SNPs on the SNP array approximately 12% dropped out. For the two potato mapping populations 165 and 185 SNPs segregating SNP loci could be mapped on the respective genetic maps, illustrating the effectiveness of our pipeline for SNP selection and validation. The online version of this article (doi:10.1007/s11032-009-9377-5) contains supplementary material, which is available to authorized users.
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影响因子：
2.9
作者：
Ching A;Caldwell KS;Jung M;Dolan M;Smith OS;Tingey S;Morgante M;Rafalski AJ
通讯作者：
Rafalski AJ
DOI：
10.1101/sqb.2003.68.69
发表时间：
2003-01-01
期刊：
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影响因子：
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作者：
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通讯作者：
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作者：
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Edwards, D
影响因子：
30.8
作者：
Syvänen, AC
通讯作者：
Syvänen, AC
影响因子：
5.4
作者：
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通讯作者：
Lorenzen, J