SNPnexus: a web database for functional annotation of newly discovered and public domain single nucleotide polymorphisms.
SNPnexus: a web database for functional annotation of newly discovered and public domain single nucleotide polymorphisms.
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DOI：
10.1093/bioinformatics/btn653
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发表时间：
2009-03-01
期刊：
影响因子：
--
通讯作者：
Lemoine NR
中科院分区：
文献类型：
--
作者：
Chelala C;Khan A;Lemoine NR
动机：设计一种新的计算工具，使科学家能够对新发现的和公共领域的单核苷酸多态性进行功能性注释，以帮助在进一步的疾病研究和大规模基因分型项目中优先考虑目标。SNPnexus数据库为新的和公开的SNPs提供了功能注释。转录组和蛋白质组水平的可能影响的特点和报告，从五个主要的注释系统提供最广泛的信息选择性剪接。还可以检索关于HapMap基因型和等位基因频率、与潜在调控元件或结构变异的重叠以及相关遗传疾病的其他信息。SNPnexus数据库具有用户友好的Web界面，使用dbSNP的SNP标识符以及克隆、重叠群或染色体上的基因组位置提供单个或批量查询选项。因此，SNPnexus是目前唯一一个提供公共数据库和测序项目中新发现的SNP的完整功能注释的数据库。因此，我们描述了SNPnexus，提供了查询选项的详细信息，注释类别以及使用的生物学示例。可用性：SNPnexus数据库可在http://www.snp-nexus.org上免费获取。联系人：claude. cancer.org.uk
Motivation: Design a new computational tool allowing scientists to functionally annotate newly discovered and public domain single nucleotide polymorphisms in order to help in prioritizing targets in further disease studies and large-scale genotyping projects. Summary: SNPnexus database provides functional annotation for both novel and public SNPs. Possible effects on the transcriptome and proteome levels are characterized and reported from five major annotation systems providing the most extensive information on alternative splicing. Additional information on HapMap genotype and allele frequency, overlaps with potential regulatory elements or structural variations as well as related genetic diseases can be also retrieved. The SNPnexus database has a user-friendly web interface, providing single or batch query options using SNP identifiers from dbSNP as well as genomic location on clones, contigs or chromosomes. Therefore, SNPnexus is the only database currently providing a complete set of functional annotations of SNPs in public databases and newly detected from sequencing projects. Hence, we describe SNPnexus, provide details of the query options, the annotation categories as well as biological examples of use. Availability: The SNPnexus database is freely available at http://www.snp-nexus.org. Contact: claude.chelala@cancer.org.uk
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影响因子：
14.9
作者：
Ramensky, V;Bork, P;Sunyaev, S
通讯作者：
Sunyaev, S
影响因子：
64.8
作者：
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通讯作者：
Skol, Andrew
影响因子：
7.7
作者：
Chelala, Claude;Duchatelet, Sabine;Julier, Cecile
通讯作者：
Julier, Cecile
影响因子：
14.9
作者：
Griffiths-Jones, S
通讯作者：
Griffiths-Jones, S
影响因子：
30.8
作者：
Iafrate, AJ;Feuk, L;Lee, C
通讯作者：
Lee, C