使用Blocks数据库服务器在蛋白质同源性检测方面表现卓越。
Superior performance in protein homology detection with the Blocks Database servers.
作者信息
Henikoff S, Pietrokovski S, Henikoff J G
机构信息
Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109-1024, USA.
出版信息
Nucleic Acids Res. 1998 Jan 1;26(1):309-12. doi: 10.1093/nar/26.1.309.
The Blocks Database World Wide Web (http://www.blocks.fhcrc.org ) and Email (blocks@blocks.fhcrc.org) servers provide tools for the detection and analysis of protein homology based on alignment blocks representing conserved regions of proteins. During the past year, searching has been augmented by supplementation of the Blocks Database with blocks from the Prints Database, for a total of 4754 blocks from 1163 families. Blocks from both the Blocks and Prints Databases and blocks that are constructed from sequences submitted to Block Maker can be used for blocks-versus-blocks searching of these databases with LAMA, and for viewing logos and bootstrap trees. Sensitive searches of up-to-date protein sequence databanks are carried out via direct links to the MAST server using position-specific scoring matrices and to the BLAST and PSI-BLAST servers using consensus-embedded sequence queries. Utilizing the trypsin family to evaluate performance, we illustrate the superiority of blocks-based tools over expert pairwise searching or Hidden Markov Models.
“模块数据库”的万维网服务器（http://www.blocks.fhcrc.org ）和电子邮件服务器（blocks@blocks.fhcrc.org）提供了一些工具，用于基于代表蛋白质保守区域的比对模块来检测和分析蛋白质同源性。在过去一年中，通过将“印记数据库”中的模块补充到“模块数据库”中，搜索功能得到了增强，目前共有来自1163个家族的4754个模块。“模块数据库”和“印记数据库”中的模块以及由提交给“模块生成器”的序列构建的模块，均可用于使用LAMA对这些数据库进行模块对模块的搜索，以及查看序列标识和自引导树。通过使用特定位置评分矩阵直接链接到MAST服务器，以及使用嵌入共有序列的查询直接链接到BLAST和PSI-BLAST服务器，可对最新的蛋白质序列数据库进行灵敏搜索。利用胰蛋白酶家族来评估性能，我们展示了基于模块的工具相对于专家成对搜索或隐马尔可夫模型的优越性。
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