MolliGen, a database dedicated to the comparative genomics of Mollicutes
MolliGen, a database dedicated to the comparative genomics of Mollicutes
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DOI：
10.1093/nar/gkh114
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发表时间：
2004-01-01
影响因子：
14.9
通讯作者：
Blanchard, A
中科院分区：
文献类型：
--
作者：
Barré, A;de Daruvar, A;Blanchard, A
属于软体动物纲的细菌是最先被选择进行完整基因组测序的细菌之一，因为它们的基因组很小，并且对人类和多种动植物具有致病性。目前，已公开发布了六种基因组序列（生殖支原体、肺炎支原体、解脲支原体、肺支原体、穿透支原体和鸡毒支原体），并且随着可用软体动物基因组数量的增加，该模型生物组内的比较基因组学分析变得越来越多 具有指导意义。然而，如果没有合适的平台不仅收集原始注释，还收集公共数据库中可用的或通过应用常见生物信息学方法获得的相关信息，这样的分析很难进行。为了解决这些困难，我们开发了一个可通过网络访问的数据库，名为 MolliGen (http://cbi.labri.fr/outils/molligen/)。选择一组基因组后，用户可以根据注释、染色体上的位置或序列相似性启动各种类型的搜索。此外，已经预先计算了假定的直系同源关系，以允许差异基因组查询。结果以表格形式呈现，具有公共数据库和生物信息学分析（例如多重比对或 BLAST 搜索）的多个链接。还开发了用于结果图形可视化的特定工具，包括用于显示带有可点击对象的动态图片以及用于查看预先计算的相似性关系的多基因组浏览器。 MolliGen 旨在整合软体动物的所有完整基因组（当它们可用时）。
Bacteria belonging to the class Mollicutes were among the first ones to be selected for complete genome sequencing because of the minimal size of their genomes and their pathogenicity for humans and a broad range of animals and plants. At this time six genome sequences have been publicly released (Mycoplasma genitalium, Mycoplasma pneumoniae, Ureaplasma urealyticum-parvum, Mycoplasma pulmonis, Mycoplasma penetrans and Mycoplasma gallisepticum) and as the number of available mollicute genomes increases, comparative genomics analysis within this model group of organisms becomes more and more instructive. However, such an analysis is difficult to carry out without a suitable platform gathering not only the original annotations but also relevant information available in public databases or obtained by applying common bioinformatics methods. With the aim of solving these difficulties, we have developed a web-accessible database named MolliGen (http://cbi.labri.fr/outils/molligen/). After selecting a set of genomes the user can launch various types of search based on annotation, position on the chromosomes or sequence similarity. In addition, relationships of putative orthology have been pre-computed to allow differential genome queries. The results are presented in table format with multiple links to public databases and to bioinformatic analyses such as multiple alignments or BLAST search. Specific tools were also developed for the graphical visualization of the results, including a multi-genome browser for displaying dynamic pictures with clickable objects and for viewing relationships of precomputed similarity. MolliGen is designed to integrate all the complete genomes of mollicutes as they become available.