Worley K C, Wiese B A, Smith R F
Department of Molecular and Human Genetics, W.M. Keck Center for Computational Biology, Baylor College of Medicine, Houston, Texas 77030, USA.
Genome Res. 1995 Sep;5(2):173-84. doi: 10.1101/gr.5.2.173.
BEAUTY (BLAST enhanced alignment utility) is an enhanced version of the NCBI's BLAST data base search tool that facilitates identification of the functions of matched sequences. We have created new data bases of conserved regions and functional domains for protein sequences in NCBI's Entrez data base, and BEAUTY allows this information to be incorporated directly into BLAST search results. A Conserved Regions Data Base, containing the locations of conserved regions within Entrez protein sequences, was constructed by (1) clustering the entire data base into families, (2) aligning each family using our PIMA multiple sequence alignment program, and (3) scanning the multiple alignments to locate the conserved regions within each aligned sequence. A separate Annotated Domains Data Base was constructed by extracting the locations of all annotated domains and sites from sequences represented in the Entrez, PROSITE, BLOCKS, and PRINTS data bases. BEAUTY performs a BLAST search of those Entrez sequences with conserved regions and/or annotated domains. BEAUTY then uses the information from the Conserved Regions and Annotated Domains data bases to generate, for each matched sequence, a schematic display that allows one to directly compare the relative locations of (1) the conserved regions, (2) annotated domains and sites, and (3) the locally aligned regions matched in the BLAST search. In addition, BEAUTY search results include World-Wide Web hypertext links to a number of external data bases that provide a variety of additional types of information on the function of matched sequences. This convenient integration of protein families, conserved regions, annotated domains, alignment displays, and World-Wide Web resources greatly enhances the biological informativeness of sequence similarity searches. BEAUTY searches can be performed remotely on our system using the "BCM Search Launcher" World-Wide Web pages (URL is < http:/ /gc.bcm.tmc.edu:8088/ search-launcher/launcher.html > ).
BEAUTY（BLAST增强比对工具）是美国国立生物技术信息中心（NCBI）的BLAST数据库搜索工具的增强版本，它有助于识别匹配序列的功能。我们在NCBI的Entrez数据库中创建了蛋白质序列保守区域和功能域的新数据库，BEAUTY允许将这些信息直接纳入BLAST搜索结果。通过以下步骤构建了保守区域数据库，该数据库包含Entrez蛋白质序列中保守区域的位置：（1）将整个数据库聚类为家族；（2）使用我们的PIMA多序列比对程序比对每个家族；（3）扫描多序列比对以定位每个比对序列中的保守区域。通过从Entrez、PROSITE、BLOCKS和PRINTS数据库中代表的序列中提取所有注释域和位点的位置，构建了一个单独的注释域数据库。BEAUTY对那些具有保守区域和/或注释域的Entrez序列进行BLAST搜索。然后，BEAUTY使用来自保守区域数据库和注释域数据库的信息，为每个匹配序列生成一个示意图显示，使人们能够直接比较以下各项的相对位置：（1）保守区域；（2）注释域和位点；（3）在BLAST搜索中匹配的局部比对区域。此外，BEAUTY搜索结果包括指向多个外部数据库的万维网超文本链接，这些数据库提供了关于匹配序列功能的各种其他类型的信息。蛋白质家族、保守区域、注释域、比对显示和万维网资源的这种便捷整合极大地提高了序列相似性搜索的生物学信息含量。可以使用“BCM搜索启动器”万维网页面（网址为<http:/ /gc.bcm.tmc.edu:8088/ search-launcher/launcher.html >）在我们的系统上远程执行BEAUTY搜索。
