Database indexing for production MegaBLAST searches.
Database indexing for production MegaBLAST searches.
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DOI：
10.1093/bioinformatics/btn322
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发表时间：
2008-08-15
期刊：
影响因子：
--
通讯作者：
Schäffer AA
中科院分区：
文献类型：
--
作者：
Morgulis A;Coulouris G;Raytselis Y;Madden TL;Agarwala R;Schäffer AA
动机：用于序列比较的BLAST软件包通过将查询序列预处理到查找表中来加速同源性搜索。许多研究表明，对数据库进行预处理反而会带来更好的性能。然而，预处理数据库的序列比较方法的生产使用已被限制于程序，如BLAT和SSAHA，其被设计为当查询和数据库序列高度相似时找到匹配。结果如下：我们开发了一个新版本的MegaBLAST模块的BLAST，它的初始阶段是通过搜索数据库索引来找到匹配的短种子。我们还开发了一个程序makembindex，它将数据库预处理成一个数据结构，用于快速搜索种子。我们表明，新的“索引MegaBLAST”是最实际的使用速度比“非索引”的版本。我们表明，索引MegaBLAST是速度比miBLAST，另一种实现的BLAST核苷酸搜索与预处理数据库，我们测试的200个查询的大部分。为了部署索引MegaBLAST作为NCBI的Web BLAST服务的一部分，修改了数据库的存储和查询机制，因此一些机器现在专用于为特定数据库提供查询服务。这样的Web查询的响应时间现在比每台计算机处理多个数据库的查询时要快。可用性：索引MegaBLAST的代码是NCBI C++工具包中blacklist程序的一部分。预处理程序makembindex也在工具包中。自2007年10月以来，索引MegaBLAST已被用于NCBI的Web BLAST服务的生产中，以搜索人类和小鼠基因组的一个版本。用于执行下述测试的blaSync和makembindex的Linux命令行可执行文件、文档和一些查询集可在以下目录中获得：ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/indexed_megablast联系方式：schaffer@helix.nih.gov补充信息：补充数据可在Bioinformatics online获得。
Motivation: The BLAST software package for sequence comparison speeds up homology search by preprocessing a query sequence into a lookup table. Numerous research studies have suggested that preprocessing the database instead would give better performance. However, production usage of sequence comparison methods that preprocess the database has been limited to programs such as BLAT and SSAHA that are designed to find matches when query and database subsequences are highly similar. Results: We developed a new version of the MegaBLAST module of BLAST that does the initial phase of finding short seeds for matches by searching a database index. We also developed a program makembindex that preprocesses the database into a data structure for rapid seed searching. We show that the new ‘indexed MegaBLAST’ is faster than the ‘non-indexed’ version for most practical uses. We show that indexed MegaBLAST is faster than miBLAST, another implementation of BLAST nucleotide searching with a preprocessed database, for most of the 200 queries we tested. To deploy indexed MegaBLAST as part of NCBI'sWeb BLAST service, the storage of databases and the queueing mechanism were modified, so that some machines are now dedicated to serving queries for a specific database. The response time for such Web queries is now faster than it was when each computer handled queries for multiple databases. Availability: The code for indexed MegaBLAST is part of the blastn program in the NCBI C++ toolkit. The preprocessor program makembindex is also in the toolkit. Indexed MegaBLAST has been used in production on NCBI's Web BLAST service to search one version of the human and mouse genomes since October 2007. The Linux command-line executables for blastn and makembindex, documentation, and some query sets used to carry out the tests described below are available in the directory: ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/indexed_megablast Contact: schaffer@helix.nih.gov Supplementary information: Supplementary data are available at Bioinformatics online.
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