PRODOC: a resource for the comparison of tethered protein domain architectures with in-built information on remotely related domain families.
PRODOC: a resource for the comparison of tethered protein domain architectures with in-built information on remotely related domain families.
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DOI：
10.1093/nar/gki474
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发表时间：
2005-07-01
影响因子：
14.9
通讯作者：
Srinivasan, N
中科院分区：
文献类型：
--
作者：
Krishnadev, O;Rekha, N;Pandit, SB;Abhiman, S;Mohanty, S;Swapna, LS;Gore, S;Srinivasan, N
蛋白质结构域组织和比较 (PRODOC) 包含多个程序，可以方便地将蛋白质作为结构域序列进行比较。内置数据集目前包含来自 192 个生物体的约 698 000 个蛋白质，具有完整的基因组数据，以及从 Pfam 数据库获得的所有 SWISSPROT 蛋白质。 PRODOC 中的所有条目都表示为功能域序列，使用隐马尔可夫模型分配，而不是氨基酸序列。蛋白质组中平均 69% 的蛋白质和 49% 的残基被功能域分配覆盖。软件工具允许用户查询具有域序列的数据集，并识别具有相同或混乱或循环排列的域排列的蛋白质。由于有人提出具有混乱或相同结构域序列的蛋白质具有相似的功能，因此该搜索工具可用于分配多结构域蛋白质的整体功能。 PRODOC 的独特功能包括根据结构域序列和形成超家族的远亲结构域家族的内置信息生成多结构域蛋白质之间的比对。还可以使用 PRODOC 来识别跨生物体的域共享和基因融合事件。 PRODOC 中详尽的基因组-基因组比较工具还可以检测两个生物体之间连续的域共享和域融合事件。该工具可以识别两个密切相关的生物体中参与相似生物过程的基因簇。 PRODOC 的 URL 是 。
PROtein Domain Organization and Comparison (PRODOC) comprises several programs that enable convenient comparison of proteins as a sequence of domains. The in-built dataset currently consists of ∼698 000 proteins from 192 organisms with complete genomic data, and all the SWISSPROT proteins obtained from the Pfam database. All the entries in PRODOC are represented as a sequence of functional domains, assigned using hidden Markov models, instead of as a sequence of amino acids. On average 69% of the proteins in the proteomes and 49% of the residues are covered by functional domain assignments. Software tools allow the user to query the dataset with a sequence of domains and identify proteins with the same or a jumbled or circularly permuted arrangement of domains. As it is proposed that proteins with jumbled or the same domain sequences have similar functions, this search tool is useful in assigning the overall function of a multi-domain protein. Unique features of PRODOC include the generation of alignments between multi-domain proteins on the basis of the sequence of domains and in-built information on distantly related domain families forming superfamilies. It is also possible using PRODOC to identify domain sharing and gene fusion events across organisms. An exhaustive genome–genome comparison tool in PRODOC also enables the detection of successive domain sharing and domain fusion events across two organisms. The tool permits the identification of gene clusters involved in similar biological processes in two closely related organisms. The URL for PRODOC is .
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