Predicting Gene Ontology functions from ProDom and CDD protein domains
Predicting Gene Ontology functions from ProDom and CDD protein domains
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DOI：
10.1101/gr.222902
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发表时间：
2002-04-01
期刊：
影响因子：
7
通讯作者：
Stoeckert, CJ
中科院分区：
文献类型：
--
作者：
Schug, J;Diskin, S;Stoeckert, CJ
描述了一种启发式算法，用于将基因本体 (GO) 定义的分子功能与 ProDom 和 CDD 数据库中列出的蛋白质结构域相关联。该算法根据 GO 联盟分配给基因产物的功能交集生成功能域关联规则，其中包含不同序列相似性水平的 ProDom 和/或 CDD 域。 GO 分子函数的层次性质被纳入规则生成中。对生成的规则子集进行手动审核表明，ProDom 规则的准确率为 87%，CDD 规则的准确率为 84%。这些关联的用途是，如果与一个或多个GO功能已关联的ProDom或CDD结构域存在足够的相似性，则可以为新序列分配推定的功能。尽管越来越多地对模式生物的基因产物进行功能分配，但研究人员的需求可能会继续超过管理者的努力，特别是对于非模式生物。与其他方法在覆盖率和一致性方面进行了比较，表明了该方法的实用性。域功能关联和功能分配可从我们的网站 http://www.cbil.upeinn.edu/GO 获取。
A heuristic algorithm for associating Gene Ontology (GO) defined molecular functions to protein domains as listed in the ProDom and CDD databases is described. The algorithm generates rules for function-domain associations based on the intersection of functions assigned to gene products by the GO consortium that contain ProDom and/or CDD domains at varying levels of sequence similarity. The hierarchical nature of GO molecular functions is incorporated into rule generation. Manual review of a subset of the rules generated indicates an accuracy rate of 87% for ProDom rules and 84% for CDD rules. The utility of these associations is that novel sequences can be assigned a putative function if sufficient similarity exists to a ProDom or CDD domain for which one or more GO functions has been associated. Although functional assignments are increasingly being made for gene products from model organisms, it is likely that the needs of investigators will continue to outpace the efforts of curators, particularly for nonmodel organisms. A comparison with other methods in terms of coverage and agreement was performed, indicating the utility of the approach. The domain-function associations and function assignments are available from our website http:// www.cbil.upeinn.edu/GO.