SIMAP--a comprehensive database of pre-calculated protein sequence similarities, domains, annotations and clusters.
SIMAP--a comprehensive database of pre-calculated protein sequence similarities, domains, annotations and clusters.
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DOI：
10.1093/nar/gkp949
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发表时间：
2010-01
影响因子：
14.9
通讯作者：
Mewes HW
中科院分区：
文献类型：
--
作者：
Rattei T;Tischler P;Götz S;Jehl MA;Hoser J;Arnold R;Conesa A;Mewes HW
利用序列比较预测蛋白质功能和重建进化起源仍然是序列分析中最有力的工具。由于已知蛋白质序列数量的指数增长和随后相似性矩阵的二次增长，蛋白质相似性矩阵（SIMAP）的计算成为一项计算密集型任务。SIMAP数据库提供了蛋白质序列相似性矩阵、基于序列的特征和序列聚类的全面和最新的预先计算。截至2009年9月，SIMAP涵盖了4800万个蛋白质和超过2300万个非冗余序列。SIMAP的新特征包括通过包括数据库如ENSEMBL来扩展序列空间，以及基于宏基因组的一致处理和注释来整合宏基因组。此外，Blast 2GO对SIMAP中所有序列的蛋白质功能预测都进行了预先计算，数据访问和查询功能也得到了改进。SIMAP帮助生物学家系统地查询最新的序列空间，并促进计算生物学中的大规模下游项目。通过个人门户网站（http：//mips.gsf.de/simap/）和DAS（http：//webclu.bio.wzw.tum.de/das/）和网络服务（http：//www.example.com）免费提供对SIMAP的访问mips.gsf.de/webservices/services/SimapService2.0? wsdl）。
The prediction of protein function as well as the reconstruction of evolutionary genesis employing sequence comparison at large is still the most powerful tool in sequence analysis. Due to the exponential growth of the number of known protein sequences and the subsequent quadratic growth of the similarity matrix, the computation of the Similarity Matrix of Proteins (SIMAP) becomes a computational intensive task. The SIMAP database provides a comprehensive and up-to-date pre-calculation of the protein sequence similarity matrix, sequence-based features and sequence clusters. As of September 2009, SIMAP covers 48 million proteins and more than 23 million non-redundant sequences. Novel features of SIMAP include the expansion of the sequence space by including databases such as ENSEMBL as well as the integration of metagenomes based on their consistent processing and annotation. Furthermore, protein function predictions by Blast2GO are pre-calculated for all sequences in SIMAP and the data access and query functions have been improved. SIMAP assists biologists to query the up-to-date sequence space systematically and facilitates large-scale downstream projects in computational biology. Access to SIMAP is freely provided through the web portal for individuals (http://mips.gsf.de/simap/) and for programmatic access through DAS (http://webclu.bio.wzw.tum.de/das/) and Web-Service (http://mips.gsf.de/webservices/services/SimapService2.0?wsdl).