SynBrowse: a synteny browser for comparative sequence analysis
SynBrowse: a synteny browser for comparative sequence analysis
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DOI：
10.1093/bioinformatics/bti555
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发表时间：
2005-09-01
期刊：
影响因子：
5.8
通讯作者：
Brendel, V
中科院分区：
文献类型：
--
作者：
Pan, XK;Stein, L;Brendel, V
动机：各种序列项目最近为深入测序各种系统发育所做的努力为比较序列分析提供了丰富的资源。通用且便携的工具对于科学家可视化和分析序列比较至关重要。结果：我们开发了 SynBrowse，一种同线性浏览器，用于可视化和分析物种内部和物种之间的基因组比对。它旨在帮助科学家研究序列之间的宏观同线性、微观同线性和同源基因。它还可以帮助识别物种的未表征基因、推定的调控元件和新的结构特征。 SynBrowse 是一个 GBrowse（通用基因组浏览器）系列软件工具，运行在开源 BioPerl 模块之上。它由两个组件组成：一个基于 Web 的前端和一组关系数据库后端。除了焦点序列的基因组注释之外，每个数据库还存储从焦点序列到参考序列的预先计算的比对。用户界面允许最终用户选择关键的比较比对类型，搜索两个序列之间的同线性块，并放大以详细查看相应基因组注释之间的关系。 SynBrowse是便携式的，安装简单，配置灵活，数据输入方便，易于与模型生物系统的其他组件集成。
Motivation: The recent efforts of various sequence projects to sequence deeply into various phylogenies provide great resources for comparative sequence analysis. A generic and portable tool is essential for scientists to visualize and analyze sequence comparisons.Results: We have developed SynBrowse, a synteny browser for visualizing and analyzing genome alignments both within and between species. It is intended to help scientists study macrosynteny, microsynteny and homologous genes between sequences. It can also aid with the identification of uncharacterized genes, putative regulatory elements and novel structural features of a species. SynBrowse is a GBrowse (the Generic Genome Browser) family software tool that runs on top of the open source BioPerl modules. It consists of two components: a web-based front end and a set of relational database back ends. Each database stores pre-computed alignments from a focus sequence to reference sequences in addition to the genome annotations of the focus sequence. The user interface lets end users select a key comparative alignment type and search for syntenic blocks between two sequences and zoom in to view the relationships among the corresponding genome annotations in detail. SynBrowse is portable with simple installation, flexible configuration, convenient data input and easy integration with other components of a model organism system.