Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8W 3P6, Canada.
Department of Computer Science, University of Victoria, Victoria, BC, V8W 3P6, Canada.
Viruses. 2010 Sep;2(9):1867-1885. doi: 10.3390/v2091867. Epub 2010 Aug 31.
We describe the use of Java Pattern Finder (JaPaFi) to identify short (<100 nt) highly conserved sequences in a series of poxvirus genomes. The algorithm utilizes pattern matching to identify approximate matches appearing at least once in each member of a set of genomes; a key feature is that the genomes do not need to be aligned. The user simply specifies the genomes to search, minimum length of sequences to find and the maximum number of mismatches and indels allowed. Many of the most highly conserved segments contain poxvirus promoter elements.
我们描述了 Java 模式查找器 (JaPaFi) 在一系列痘病毒基因组中识别短（<100nt）高度保守序列的用途。该算法利用模式匹配来识别出在一组基因组中的每个成员中至少出现一次的近似匹配；一个关键特征是，基因组不需要对齐。用户只需指定要搜索的基因组、要找到的最短序列长度以及允许的最大错配和插入缺失数量。许多高度保守的片段包含痘病毒启动子元件。
