XplorSeq: A software environment for integrated management and phylogenetic analysis of metagenomic sequence data
XplorSeq: A software environment for integrated management and phylogenetic analysis of metagenomic sequence data
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DOI：
10.1186/1471-2105-9-420
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发表时间：
2008-10-07
影响因子：
3
通讯作者：
Frank, Daniel N.
中科院分区：
文献类型：
--
作者：
Frank, Daniel N.
背景资料：自动化DNA测序技术的进步加速了宏基因组DNA序列的产生，特别是环境核糖体RNA基因（rDNA）序列。随着基于rDNA的微生物生态学研究的规模不断扩大，出现了对能够管理，注释和分析在这些projects.Results积累了过多的不同数据的软件的需求：XplorSeq是一个软件包，便于DNA序列的编译，管理和系统发育分析。XplorSeq被开发用于但不限于环境rRNA基因序列的高通量分析。XplorSeq通过使用基于Macintosh OS-X的图形用户界面（GUI）集成和扩展了几种常用的基于UNIX的分析工具。通过该GUI，用户可以执行基本序列导入和组装步骤（碱基调用、载体/引物修剪、重叠群组装），执行BLAST（基本局部比对和搜索工具; [1-3]）搜索NCBI和本地数据库，创建多个序列比对，构建系统发育树，组装操作分类单位，估计生物多样性指数，并以各种格式汇总数据。此外，序列可以用用户指定的元数据进行注释，然后可以用于对数据进行分类并组织分析和报告。一个基于文档的架构允许并行分析的序列数据从多个克隆或扩增子，序列和其他数据存储在一个单一的file.Conclusion：XplorSeq应该有利于研究人员谁是从事环境序列数据的分析，特别是那些使用生物信息学软件的经验很少。虽然XplorSeq是为管理rDNA序列数据而开发的，但它可以应用于大多数测序项目。该应用程序可在http://vent.colorado.edu/phyloware上免费用于非商业用途。
Background: Advances in automated DNA sequencing technology have accelerated the generation of metagenomic DNA sequences, especially environmental ribosomal RNA gene (rDNA) sequences. As the scale of rDNA-based studies of microbial ecology has expanded, need has arisen for software that is capable of managing, annotating, and analyzing the plethora of diverse data accumulated in these projects.Results: XplorSeq is a software package that facilitates the compilation, management and phylogenetic analysis of DNA sequences. XplorSeq was developed for, but is not limited to, high-throughput analysis of environmental rRNA gene sequences. XplorSeq integrates and extends several commonly used UNIX-based analysis tools by use of a Macintosh OS-X-based graphical user interface (GUI). Through this GUI, users may perform basic sequence import and assembly steps (base-calling, vector/primer trimming, contig assembly), perform BLAST ( Basic Local Alignment and Search Tool; [1-3]) searches of NCBI and local databases, create multiple sequence alignments, build phylogenetic trees, assemble Operational Taxonomic Units, estimate biodiversity indices, and summarize data in a variety of formats. Furthermore, sequences may be annotated with user-specified meta-data, which then can be used to sort data and organize analyses and reports. A document-based architecture permits parallel analysis of sequence data from multiple clones or amplicons, with sequences and other data stored in a single file.Conclusion: XplorSeq should benefit researchers who are engaged in analyses of environmental sequence data, especially those with little experience using bioinformatics software. Although XplorSeq was developed for management of rDNA sequence data, it can be applied to most any sequencing project. The application is available free of charge for non-commercial use at http://vent.colorado.edu/phyloware.