A phylogenomic gene cluster resource: the Phylogenetically Inferred Groups (PhIGs) database.
A phylogenomic gene cluster resource: the Phylogenetically Inferred Groups (PhIGs) database.
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DOI：
10.1186/1471-2105-7-201
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发表时间：
2006-04-11
影响因子：
3
通讯作者：
Boore JL
中科院分区：
文献类型：
--
作者：
Dehal PS;Boore JL
我们在这里介绍了PhIGs数据库，一个用于测序基因组的基因组数据库。虽然存在许多方法来聚类基因家族，但很少有人试图创建真正的直系同源簇，这些直系同源簇在进化深度范围内共享来自单个祖先基因的血统。虽然这些非系统发育的基因家族簇已被广泛用于基因注释，但已知错误是由缓慢进化的旁系同源物的人为关联和缺乏对那些更快速进化的旁系同源物的注释而引入的。一个完整的系统发育框架是必要的功能的准确推断和许多研究，解决模式和机制的基因组进化。进化基因簇的自动生成、基因树的创建、直系和旁系关系的确定以及这些信息与基因注释、表达信息和基因组背景的相关性是科学界的重要资源。PhIGs数据库目前包含23个完整测序的真菌和后生动物基因组，包含409，653个基因，这些基因被分为42，645个基因簇。构建每个基因簇，使得基因序列距离与已知的生物体关系一致，并且这样做，最大化簇代表真正直向同源基因的可能性。PhIGs网站包含的工具允许通过注释上的关键字搜索（如GO和InterPro分配）以及BLAST和HMM的序列相似性搜索来研究其系统发育框架内的基因。除了显示每个簇中基因的进化关系外，该网站还允许用户查看特定基因组中同源基因的相对物理位置。基因和基因组的准确分析只能在其完整的系统发育背景下进行。PhIGs数据库和相应的网站为科学界解决了这个问题。我们的目标是随着更多的基因组被测序而扩展内容，并使用这个框架来整合更多的分析。
We present here the PhIGs database, a phylogenomic resource for sequenced genomes. Although many methods exist for clustering gene families, very few attempt to create truly orthologous clusters sharing descent from a single ancestral gene across a range of evolutionary depths. Although these non-phylogenetic gene family clusters have been used broadly for gene annotation, errors are known to be introduced by the artifactual association of slowly evolving paralogs and lack of annotation for those more rapidly evolving. A full phylogenetic framework is necessary for accurate inference of function and for many studies that address pattern and mechanism of the evolution of the genome. The automated generation of evolutionary gene clusters, creation of gene trees, determination of orthology and paralogy relationships, and the correlation of this information with gene annotations, expression information, and genomic context is an important resource to the scientific community. The PhIGs database currently contains 23 completely sequenced genomes of fungi and metazoans, containing 409,653 genes that have been grouped into 42,645 gene clusters. Each gene cluster is built such that the gene sequence distances are consistent with the known organismal relationships and in so doing, maximizing the likelihood for the clusters to represent truly orthologous genes. The PhIGs website contains tools that allow the study of genes within their phylogenetic framework through keyword searches on annotations, such as GO and InterPro assignments, and sequence similarity searches by BLAST and HMM. In addition to displaying the evolutionary relationships of the genes in each cluster, the website also allows users to view the relative physical positions of homologous genes in specified sets of genomes. Accurate analyses of genes and genomes can only be done within their full phylogenetic context. The PhIGs database and corresponding website address this problem for the scientific community. Our goal is to expand the content as more genomes are sequenced and use this framework to incorporate more analyses.
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影响因子：
7
作者：
Lee, Y;Sultana, R;Quackenbush, J
通讯作者：
Quackenbush, J
DOI：
10.2307/2412448
发表时间：
1970-01-01
期刊：
SYSTEMATIC ZOOLOGY
影响因子：
--
作者：
FITCH, WM
通讯作者：
FITCH, WM
影响因子：
5.8
作者：
Zdobnov, EM;Apweiler, R
通讯作者：
Apweiler, R
影响因子：
9.8
作者：
Dehal P;Boore JL
通讯作者：
Boore JL
影响因子：
3
作者：
Dehal PS;Boore JL
通讯作者：
Boore JL