Protein function prediction using the Protein Link EXplorer (PLEX)
Protein function prediction using the Protein Link EXplorer (PLEX)
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DOI：
10.1093/bioinformatics/bti313
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发表时间：
2005-05-15
期刊：
影响因子：
5.8
通讯作者：
Marcotte, EM
中科院分区：
文献类型：
--
作者：
Date, SV;Marcotte, EM
我们介绍了蛋白质链接浏览器(PLEX)，这是一个基于网络的环境，可以为任何给定的氨基酸序列构建系统发育谱，并将其与89个基因组中近35万个预测基因的谱进行比较，作为交互识别功能连锁基因和预测蛋白质功能的手段。Plex可以迭代搜索，还可以搜索染色体基因邻居和Rosetta Stone链接。Plex搜索结果伴随着对连锁置信度的定量估计，使用户能够利用基于共同遗传、操纵子和基因融合的方法来推断基因功能和重建细胞系统和途径。
We introduce the Protein Link EXplorer (PLEX), a web-based environment that allows the construction of a phylogenetic profile for any given amino acid sequence, and its comparison with profiles of similar to 350 000 predicted genes from 89 genomes, as a means of interactively identifying functionally linked genes and predicting protein function. PLEX can be searched iteratively and also enables searches for chromosomal gene neighbors and Rosetta Stone linkages. PLEX search results are accompanied by quantitative estimates of linkage confidence, enabling users to take advantage of coinheritance, operon and gene fusion-based methods for inferring gene function and reconstructing cellular systems and pathways.