genBlastA: Enabling BLAST to identify homologous gene sequences
genBlastA: Enabling BLAST to identify homologous gene sequences
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DOI：
10.1101/gr.082081.108
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发表时间：
2009-01-01
期刊：
影响因子：
7
通讯作者：
Chen, Nansheng
中科院分区：
文献类型：
--
作者：
She, Rong;Chu, Jeffrey S. -C.;Chen, Nansheng
BLAST是一种广泛使用的用于识别同源序列的局部相似性搜索工具。当基因序列（蛋白质序列或核苷酸序列）用作查询以搜索基因组中的同源序列时，表示为高得分对（HSP）列表的搜索结果是候选基因的片段而不是全长候选基因。代表靶基因组序列中候选基因的相关HSP（“信号”）隐藏在报告中，该报告还包含数百至数千个随机HSP（“噪声”）。因此，BLAST结果往往是压倒性的和混乱的，即使是有经验的用户。为了有效地使用BLAST，需要一个程序来从整个HSP报告中提取代表候选同源基因的相关HSP。为了实现这一目标，我们设计了一种基于图的算法genBlastA，它自动将HSP筛选到定义明确的组中，每个组代表靶基因组中的一个候选基因。genBlastA的新奇是反映一组生物学动机要求的边长度量，使得每个最短路径对应于代表同源基因的HSP组。我们已经证明，这种新的算法是高效和准确的同源序列识别，它优于现有的方法具有类似的功能。
BLAST is an extensively used local similarity search tool for identifying homologous sequences. When a gene sequence (either protein sequence or nucleotide sequence) is used as a query to search for homologous sequences in a genome, the search results, represented as a list of high-scoring pairs (HSPs), are fragments of candidate genes rather than full-length candidate genes. Relevant HSPs ("signals"), which represent candidate genes in the target genome sequences, are buried within a report that contains also hundreds to thousands of random HSPs ("noises"). Consequently, BLAST results are often overwhelming and confusing even to experienced users. For effective use of BLAST, a program is needed for extracting relevant HSPs that represent candidate homologous genes from the entire HSP report. To achieve this goal, we have designed a graph-based algorithm, genBlastA, which automatically filters HSPs into well-defined groups, each representing a candidate gene in the target genome. The novelty of genBlastA is an edge length metric that reflects a set of biologically motivated requirements so that each shortest path corresponds to an HSP group representing a homologous gene. We have demonstrated that this novel algorithm is both efficient and accurate for identifying homologous sequences, and that it outperforms existing approaches with similar functionalities.