PowerBLAST: A new network BLAST application for interactive or automated sequence analysis and annotation
PowerBLAST: A new network BLAST application for interactive or automated sequence analysis and annotation
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DOI：
10.1101/gr.7.6.649
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发表时间：
1997-06-01
期刊：
影响因子：
7
通讯作者：
Madden, TL
中科院分区：
文献类型：
--
作者：
Zhang, JH;Madden, TL
随着DNA测序速度的提高，通过序列相似性搜索进行的分析将需要在灵敏度、特异性、自动化潜力和注释一致性方面变得更加有效。PowerBLAST的开发部分是为了解决这些问题。PowerBLAST包括许多用于掩蔽重复元素和低复杂性序列的选项。它还能够将搜索限制在NCBI分类索引的任何级别，从而支持“比较基因组学”应用。当查询序列的一个区域与多个数据库序列匹配时，使用SIM系列算法对BLAST输出进行后处理产生最佳、空位比对和多重比对。PowerBLAST能够处理任何长度的序列，因为它将长查询序列划分为重叠片段，然后在搜索后合并结果。结果可以以图形方式、文本形式或带有GenBank和Google Z链接的HTML页面查看。对于匹配数据库序列，注释特征叠加在输出中的对齐查询序列上，从而大大增加了解释的容易性。这样的特征可以用于新序列的自动注释，因为ASN. 1形式的PowerBLAST输出可以“拖放”到NCBI的Sequin程序中用于序列注释和提交。PowerBLAST能够在NCBI的BLAST服务器上在60分钟内分析和注释100-kb的查询。
As the rate of DNA sequencing increases, analysis by sequence similarity search will need to become much more efficient in terms of sensitivity, specificity, automation potential, and consistency in annotation. PowerBLAST was developed, in part, to address these problems. PowerBLAST includes a number of options for masking repetitive elements and low complexity subsequences. It also has the capacity to restrict the search to any level of NCBI's taxonomy index, thus supporting ''comparative genomics'' applications. Postprocessing of the BLAST output using the SIM series of algorithms produces optimal, gapped alignments, and multiple alignments when a region of the query sequence matches multiple database sequences. PowerBLAST is capable of processing sequences of any length because it divides long query sequences into overlapping fragments and then merges the results after searching. The results may be viewed graphically, as a textual representation, or as an HTML page with links to GenBank and Entrez. For matching database sequences, annotated features are superimposed on the aligned query sequence in the output, thus greatly increasing the ease of interpretation. Such features may be used for automated annotation of new sequence because PowerBLAST output in ASN.1 form may be ''dragged and dropped'' into NCBI's Sequin program for sequence annotation and submission. PowerBLAST is capable of analyzing and annotating a 100-kb query in 60 min on NCBI's BLAST server.