NBLAST: a cluster variant of BLAST for NxN comparisons
NBLAST: a cluster variant of BLAST for NxN comparisons
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DOI：
10.1186/1471-2105-3-13
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发表时间：
2002-01-01
影响因子：
3
通讯作者：
Hogue, CWV
中科院分区：
文献类型：
--
作者：
Dumontier, M;Hogue, CWV
背景：BLAST 算法将生物序列相互比较，以确定共享的基序和共同的祖先。然而，将所有非冗余 (NR) 序列与所有其他 NR 序列进行比较是一项计算密集型任务。我们开发了 NBLAST 作为 BLAST 系列序列比较程序的集群计算机实现，目的是生成预先计算的 BLAST 比对和 NR 序列的邻居列表。结果：NBLAST 执行启发式 BLAST 算法并生成详尽的比对数据库，但它只计算可能的 N-2 个比对的 N(N - 1)/2 个比对（即上三角形），其中 N 是要比较的所有序列的集合。任务分区算法允许跨所有集群节点进行集群计算，并且 NBLAST 主进程生成 BLAST 序列比对数据库和每个序列记录的序列邻居列表。生成的序列比对和邻居数据库用于通过 C/C++ 和 PERIL 应用程序编程接口 (API) 为 SeqHound 查询系统提供服务。结论：NBLAST 为 NCBI 的远程 Entrez 系统提供了本地替代方案，用于预先计算的 BLAST 比对和邻居查询。在我们的 216 处理器 450 MHz Pill 集群上，NBLAST 需要大约 24 小时来计算当前非冗余蛋白质数据库中 850000 个蛋白质的邻居。
Background: The BLAST algorithm compares biological sequences to one another in order to determine shared motifs and common ancestry. However, the comparison of all non-redundant (NR) sequences against all other NR sequences is a computationally intensive task. We developed NBLAST as a cluster computer implementation of the BLAST family of sequence comparison programs for the purpose of generating pre-computed BLAST alignments and neighbour lists of NR sequences.Results: NBLAST performs the heuristic BLAST algorithm and generates an exhaustive database of alignments, but it only computes N(N - 1)/2 alignments (i.e. the upper triangle) of a possible N-2 alignments, where N is the set of all sequences to be compared. A task-partitioning algorithm allows for cluster computing across all cluster nodes and the NBLAST master process produces a BLAST sequence alignment database and a list of sequence neighbours for each sequence record. The resulting sequence alignment and neighbour databases are used to serve the SeqHound query system through a C/C++ and PERIL Application Programming Interface (API).Conclusions: NBLAST offers a local alternative to the NCBI's remote Entrez system for precomputed BLAST alignments and neighbour queries. On our 216-processor 450 MHz Pill cluster, NBLAST requires similar to24 hrs to compute neighbours for 850000 proteins currently in the non-redundant protein database.