Repsys Valdemaras, Margelevicius Mindaugas, Venclovas Ceslovas
Institute of Biotechnology, Graiciūno 8, LT-02241 Vilnius, Lithuania.
BMC Bioinformatics. 2008 Jun 27;9:296. doi: 10.1186/1471-2105-9-296.
Sequence searches are routinely employed to detect and annotate related proteins. However, a rapid growth of databases necessitates a frequent repetition of sequence searches and subsequent analysis of obtained results. Although there are several automatic systems available for executing periodical sequence searches and reporting results, they all suffer either from a lack of sensitivity, restrictive database choice or limited flexibility in setting up search strategies. Here, a new sequence search and reporting software package designed to address these shortcomings is described.
Re-searcher is an open-source highly configurable system for recurrent detection and reporting of new homologs for the sequence of interest in specified protein sequence databases. Searches are performed using PSI-BLAST at desired time intervals either within NCBI or local databases. In addition to searches against individual databases, the system can perform "PDB-BLAST"-like combined searches, when PSI-BLAST profile generated during search against the first database is used to search the second database. The system supports multiple users enabling each to separately keep track of multiple queries and query-specific results.
Re-searcher features a large number of options enabling automatic periodic detection of both close and distant homologs. At the same time it has a simple and intuitive interface, making the analysis of results even for a large number of queries a straightforward task.
序列搜索常用于检测和注释相关蛋白质。然而，数据库的快速增长使得序列搜索需要频繁重复，并对所得结果进行后续分析。尽管有几种自动系统可用于执行定期序列搜索并报告结果，但它们都存在灵敏度不足、数据库选择受限或设置搜索策略时灵活性有限的问题。在此，描述了一种旨在解决这些缺点的新型序列搜索和报告软件包。
Re-searcher是一个开源的、高度可配置的系统，用于在指定蛋白质序列数据库中反复检测和报告感兴趣序列的新同源物。搜索使用PSI-BLAST在所需时间间隔内针对NCBI数据库或本地数据库进行。除了针对单个数据库进行搜索外，当在针对第一个数据库的搜索过程中生成的PSI-BLAST图谱用于搜索第二个数据库时，该系统还可以执行类似“PDB-BLAST”的组合搜索。该系统支持多个用户，使每个用户能够分别跟踪多个查询和特定于查询的结果。
Re-searcher具有大量选项，能够自动定期检测密切和远距离同源物。同时，它具有简单直观的界面，即使对于大量查询，结果分析也是一项简单的任务。
