iBarcode.org: web-based molecular biodiversity analysis
iBarcode.org: web-based molecular biodiversity analysis
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DOI：
10.1186/1471-2105-10-s6-s14
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发表时间：
2009-01-01
影响因子：
3
通讯作者：
Hajibabaei, Mehrdad
中科院分区：
文献类型：
--
作者：
Singer, Gregory A. C.;Hajibabaei, Mehrdad
背景：DNA序列已成为生物多样性分析的主要信息来源。例如，短的标准化物种特异性基因组区域，DNA条形码，正在被用作物种识别和生物多样性研究的全球标准。大多数DNA条形码是由具有DNA测序专业知识但不具有生物信息学数据分析专业知识的实验室生成的。因此，我们开发了一套基于网络的工具，以帮助DNA条形码研究人员分析他们的庞大datasets.Results：我们的基于网络的工具，可在http://www.ibarcode.org，允许用户管理他们的条形码数据集，剔除非唯一序列，确定一个物种内的单倍型，并检查物种内到物种间的分歧。此外，我们还提供了一些遗传学工具，将允许用户操纵系统发育树产生的其他流行programmes.Conclusion：使用基于Web的门户网站的条形码分析是方便的，特别是因为WWW本身是平台中立的。事实上，我们甚至注意确保我们的网站可以从手持设备（如PDA和智能手机）使用。虽然iBarcode目前提供的一套工具。org是为了满足我们自己的分析需求而开发的，我们希望来自用户的反馈将激发未来工具的开发。我们也欢迎用户构建的模块，可以纳入iBarcode框架。
Background: DNA sequences have become a primary source of information in biodiversity analysis. For example, short standardized species-specific genomic regions, DNA barcodes, are being used as a global standard for species identification and biodiversity studies. Most DNA barcodes are being generated by laboratories that have an expertise in DNA sequencing but not in bioinformatics data analysis. Therefore, we have developed a web-based suite of tools to help the DNA barcode researchers analyze their vast datasets.Results: Our web-based tools, available at http://www.ibarcode.org, allow the user to manage their barcode datasets, cull out non-unique sequences, identify haplotypes within a species, and examine the within- to between-species divergences. In addition, we provide a number of phylogenetics tools that will allow the user to manipulate phylogenetic trees generated by other popular programs.Conclusion: The use of a web-based portal for barcode analysis is convenient, especially since the WWW is inherently platform-neutral. Indeed, we have even taken care to ensure that our website is usable from handheld devices such as PDAs and smartphones. Although the current set of tools available at iBarcode. org were developed to meet our own analytic needs, we hope that feedback from users will spark the development of future tools. We also welcome user-built modules that can be incorporated into the iBarcode framework.