A tool for analyzing and annotating genomic sequences
A tool for analyzing and annotating genomic sequences
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DOI：
10.1006/geno.1997.4984
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发表时间：
1997-11-15
期刊：
影响因子：
4.4
通讯作者：
Kerlavage, AR
中科院分区：
文献类型：
--
作者：
Huang, XQ;Adams, MD;Kerlavage, AR
我们描述了一个工具，用于分析和注释含有内含子的大基因组序列。分析和注释工具（AAT）包括两组程序，一组用于比较查询序列与蛋白质数据库，另一组用于比较查询序列与cDNA数据库。每一套都包含一个快速的数据库搜索程序和一个严格的比对程序。数据库搜索程序快速识别查询序列中与数据库序列相似的区域。然后，比对程序为每个区域和数据库序列构建最佳比对。比对程序还报告查询序列中外显子的坐标。将查询序列与蛋白质和cDNA数据库序列的成对比对组合成多个序列比对，其提供匹配查询区域的所有蛋白质和cDNA序列的视图。在570个DNA序列的数据集上，AAT正确识别了94%的编码核苷酸和74%的外显子。还提供了用AAT工具分析人类BAC序列的结果。AAT工具减少了定位查询序列的外显子的劳动密集型工作，并通过使用丰富的可用蛋白质和cDNA数据来改进定义内含子-外显子边界的过程。(C)北京：科学出版社.
We describe a tool for analyzing and annotating large genomic sequences containing introns. The analysis and annotation tool (AAT) includes two sets of programs, one for comparing the query sequence with a protein database and the other for comparing the query with a cDNA database. Each set contains a fast database search program and a rigorous alignment program. The database search program quickly identifies regions of the query sequence that are similar to a database sequence. Then the alignment program constructs an optimal alignment for each region and the database sequence. The alignment program also reports the coordinates of exons in the query sequence. Pairwise alignments of the query sequence with protein and cDNA database sequences are combined into multiple sequence alignments, which provide a view of all protein and cDNA sequences matching a query region. On a data set of 570 DNA sequences, AAT identified 94% of coding nucleotides correctly and 74% of exons exactly. Results of analyzing a human BAC sequence with the AAT tool are also presented. The AAT tool reduces the labor-intensive work of locating the exons of the query sequence and improves the process of defining intron-exon boundaries by using the wealth of available protein and cDNA data. (C) 1997 Academic Press.