Snpdat: easy and rapid annotation of results from de novo snp discovery projects for model and non-model organisms.
Snpdat: easy and rapid annotation of results from de novo snp discovery projects for model and non-model organisms.
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DOI：
10.1186/1471-2105-14-45
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发表时间：
2013-02-08
影响因子：
3
通讯作者：
Creevey CJ
中科院分区：
文献类型：
--
作者：
Doran AG;Creevey CJ
单核苷酸多态性（SNP）是脊椎动物和无脊椎动物中发现的最丰富的遗传变异。SNP发现已经成为一种高度自动化、稳健且相对便宜的过程，允许鉴定模型和非模型生物体的数千种突变。注释大量SNP可能是一个困难和复杂的过程。许多可用的工具被优化用于针对SNP密集采样的生物体，例如人类。目前几乎没有物种非特异性或支持非模式生物数据的工具。在这里，我们提出了SNPdat，一个高通量的分析工具，可以提供一个全面的注释的新的和已知的SNPs的任何生物体与草案序列和注释。使用高通量DNA测序在牛中鉴定的4，566个SNP的数据集，我们展示了所执行的注释和可以由SNPdat生成的统计数据。SNPdat为用户提供了一个简单的基因组注释工具，这些基因组要么不受其他工具支持，要么只有少量注释的SNP可用。SNPdat也可用于分析来自针对SNP密集采样的生物体的数据集。作为一个命令行工具，它可以很容易地被纳入现有的SNP发现管道，并填补了一个利基分析涉及非模型生物，不支持许多可用的SNP注释工具。SNPdat将引起参与SNP发现和分析项目的科学家的极大兴趣，特别是那些生物信息学经验有限的科学家。
Single nucleotide polymorphisms (SNPs) are the most abundant genetic variant found in vertebrates and invertebrates. SNP discovery has become a highly automated, robust and relatively inexpensive process allowing the identification of many thousands of mutations for model and non-model organisms. Annotating large numbers of SNPs can be a difficult and complex process. Many tools available are optimised for use with organisms densely sampled for SNPs, such as humans. There are currently few tools available that are species non-specific or support non-model organism data. Here we present SNPdat, a high throughput analysis tool that can provide a comprehensive annotation of both novel and known SNPs for any organism with a draft sequence and annotation. Using a dataset of 4,566 SNPs identified in cattle using high-throughput DNA sequencing we demonstrate the annotations performed and the statistics that can be generated by SNPdat. SNPdat provides users with a simple tool for annotation of genomes that are either not supported by other tools or have a small number of annotated SNPs available. SNPdat can also be used to analyse datasets from organisms which are densely sampled for SNPs. As a command line tool it can easily be incorporated into existing SNP discovery pipelines and fills a niche for analyses involving non-model organisms that are not supported by many available SNP annotation tools. SNPdat will be of great interest to scientists involved in SNP discovery and analysis projects, particularly those with limited bioinformatics experience.
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影响因子：
3
作者：
Goodswen SJ;Gondro C;Watson-Haigh NS;Kadarmideen HN
通讯作者：
Kadarmideen HN
影响因子：
3.7
作者：
Corona E;Dudley JT;Butte AJ
通讯作者：
Butte AJ
影响因子：
6.1
作者：
Shen TH;Carlson CS;Tarczy-Hornoch P
通讯作者：
Tarczy-Hornoch P
DOI：
10.1093/bioinformatics/btn653
发表时间：
2009-03-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Chelala C;Khan A;Lemoine NR
通讯作者：
Lemoine NR
Snap：集成的 SNP 注释平台
影响因子：
14.9
作者：
Li, Shengting;Ma, Lijia;Li, Heng;Vang, Soren;Hu, Yafeng;Bolund, Lars;Wang, Jun
通讯作者：
Wang, Jun