me-PCR: a refined ultrafast algorithm for identifying sequence-defined genomic elements
me-PCR: a refined ultrafast algorithm for identifying sequence-defined genomic elements
复制标题
DOI：
10.1093/bioinformatics/btg466
复制
发表时间：
2004-03-01
期刊：
影响因子：
5.8
通讯作者：
White, PS
中科院分区：
文献类型：
--
作者：
Murphy, K;Raj, T;White, PS
摘要：我们已经采用了最初描述的电子PCR （e-PCR）算法来执行字符串搜索，比以前可能的更准确和更快。我们的实现[多线程e-PCR (me-PCR)]运行速度足够快，甚至允许台式机器快速查询具有非常大的基因组元素集的大型基因组。此外，me-PCR是多线程的，可以解释所有IUPAC核苷酸符号，允许使用长序列（如snp）指定的元素进行搜索，接受预期PCR大小输入字段的范围，对大序列的分析需要更少的内存，并纠正一些在特殊情况下导致误报的小缺陷。因此，me-PCR为非专家实验室的复杂基因组提供了更高的注释能力。
Summary: We have adapted the originally described electronic PCR (e-PCR) algorithm to perform string searches more accurately and much more rapidly than previously possible. Our implementation [multithreaded e-PCR (me-PCR)] runs sufficiently fast to allow even desktop machines to query quickly large genomes with very large genomic element sets. In addition, me-PCR is multithreaded, interprets all IUPAC nucleotide symbols, allows searches with elements specified by long sequences (such as SNPs), accepts ranges in the expected PCR size input field, requires substantially less memory for analysis of large sequences and corrects a number of minor flaws causing misreporting of hits in exceptional cases. Thus, me-PCR provides increased annotation capabilities for complex genomes to non-expert laboratories.