Romualdi Alessandro, Felder Marius, Rose Dominic, Gausmann Ulrike, Schilhabel Markus, Glöckner Gernot, Platzer Matthias, Sühnel Jürgen
Biocomputing Group, Leibniz Institute for Age Research.
Methods Mol Biol. 2007;395:75-96.
GenColors (gencolors.fli-leibniz.de) is a new web-based software/database system aimed at an improved and accelerated annotation of prokaryotic genomes considering information on related genomes and making extensive use of genome comparison. It offers a seamless integration of data from ongoing sequencing projects and annotated genomic sequences obtained from GenBank. A variety of export/import filters manages an effective data flow from sequence assembly and manipulation programs (e.g., GAP4) to GenColors and back as well as to standard GenBank file(s). The genome comparison tools include best bidirectional hits, gene conservation, syntenies, and gene core sets. Precomputed UniProt matches allow annotation and analysis in an effective manner. In addition to these analysis options, base-specific quality data (coverage and confidence) can also be handled if available. The GenColors system can be used both for annotation purposes in ongoing genome projects and as an analysis tool for finished genomes. GenColors comes in two types, as dedicated genome browsers and as the Jena Prokaryotic Genome Viewer (JPGV). Dedicated genome browsers contain genomic information on a set of related genomes and offer a large number of options for genome comparison. The system has been efficiently used in the genomic sequencing of Borrelia garinii and is currently applied to various ongoing genome projects on Borrelia, Legionella, Escherichia, and Pseudomonas genomes. One of these dedicated browsers, the Spirochetes Genome Browser (sgb.fli-leibniz.de) with Borrelia, Leptospira, and Treponema genomes, is freely accessible. The others will be released after finalization of the corresponding genome projects. JPGV (jpgv.fli-leibniz.de) offers information on almost all finished bacterial genomes, as compared to the dedicated browsers with reduced genome comparison functionality, however. As of January 2006, this viewer includes 632 genomic elements (e.g., chromosomes and plasmids) of 293 species. The system provides versatile quick and advanced search options for all currently known prokaryotic genomes and generates circular and linear genome plots. Gene information sheets contain basic gene information, database search options, and links to external databases. GenColors is also available on request for local installation.
GenColors（gencolors.fli - leibniz.de）是一个基于网络的新型软件/数据库系统，旨在通过考虑相关基因组信息并广泛利用基因组比较，改进和加速原核生物基因组的注释。它能无缝整合来自正在进行的测序项目的数据以及从GenBank获得的已注释基因组序列。各种导入/导出过滤器管理着从序列组装和操作程序（如GAP4）到GenColors以及再返回标准GenBank文件的有效数据流。基因组比较工具包括最佳双向比对、基因保守性、共线性和基因核心集。预先计算的UniProt匹配允许进行有效的注释和分析。除了这些分析选项外，如果有可用的碱基特异性质量数据（覆盖度和置信度），也可以进行处理。GenColors系统既可以用于正在进行的基因组项目的注释，也可以作为已完成基因组的分析工具。GenColors有两种类型，即专用基因组浏览器和耶拿原核生物基因组查看器（JPGV）。专用基因组浏览器包含一组相关基因组的基因组信息，并提供大量基因组比较选项。该系统已有效地应用于加氏疏螺旋体的基因组测序，目前正应用于各种正在进行的关于疏螺旋体、军团菌、大肠杆菌和假单胞菌基因组的项目。其中一个专用浏览器，即包含疏螺旋体、钩端螺旋体和密螺旋体基因组的螺旋体基因组浏览器（sgb.fli - leibniz.de）是免费开放的。其他浏览器将在相应基因组项目完成后发布。然而，与基因组比较功能有所减少的专用浏览器相比，JPGV（jpgv.fli - leibniz.de）提供了几乎所有已完成细菌基因组的信息。截至2006年1月，该查看器包括293个物种的632个基因组元件（如染色体和质粒）。该系统为所有当前已知的原核生物基因组提供了通用的快速和高级搜索选项，并生成环状和线性基因组图谱。基因信息表包含基本的基因信息、数据库搜索选项以及到外部数据库的链接。GenColors也可应要求进行本地安装。
