ARAMEMNON, a novel database for Arabidopsis integral membrane proteins
ARAMEMNON, a novel database for Arabidopsis integral membrane proteins
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DOI：
10.1104/pp.011577
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发表时间：
2003-01-01
期刊：
影响因子：
7.4
通讯作者：
Kunze, R
中科院分区：
文献类型：
--
作者：
Schwacke, R;Schneider, A;Kunze, R
一个专门的数据库（DB）拟南芥膜蛋白，ARAMEMNON，设计，有利于基因和蛋白质序列数据的解释，通过整合功能，目前只能从个别来源。使用几种公开可用的预测程序，在拟南芥基因组DB中的大约25，500种蛋白质中鉴定出推定的整合膜蛋白。通过对来自七个程序的预测进行平均，大约6，500个蛋白质被分类为跨膜（TM）候选蛋白质。其中约有1，800座包含至少四个TM跨度，并可能与运输功能有关。ARAMEMNON DB能够直接比较7种不同TM跨度计算程序的预测和8种信号肽识别程序的亚细胞定位预测。一个特殊的函数显示与查询相关的蛋白质，并动态生成蛋白质家族结构。作为来自其他生物的第一组蛋白质，从蓝细菌集胞藻属的基因组中提取了所有约700种推定的膜蛋白，并将其并入ARAMEMNON DB中。可通过URL http://aramemnon.botanik.uni-koeln.de访问ARAMEMNON DB。
A specialized database (DB) for Arabidopsis membrane proteins, ARAMEMNON, was designed that facilitates the interpretation of gene and protein sequence data by integrating features that are presently only available from individual sources. Using several publicly available prediction programs, putative integral membrane proteins were identified among the approximately 25,500 proteins in the Arabidopsis genome DBs. By averaging the predictions from seven programs, approximately 6,500 proteins were classified as transmembrane (TM) candidate proteins. Some 1,800 of these contain at least four TM spans and are possibly linked to transport functions. The ARAMEMNON DB enables direct comparison of the predictions of seven different TM span computation programs and the predictions of subcellular localization by eight signal peptide recognition programs. A special function displays the proteins related to the query and dynamically generates a protein family structure. As a first set of proteins from other organisms, all of the approximately 700 putative membrane proteins were extracted from the genome of the cyanobacterium Synechocystis sp. and incorporated in the ARAMEMNON DB. The ARAMEMNON DB is accessible at the URL http://aramemnon.botanik.uni-koeln.de.