A web server for performing electronic PCR
A web server for performing electronic PCR
复制标题
DOI：
10.1093/nar/gkh450
复制
发表时间：
2004-07-01
影响因子：
14.9
通讯作者：
Schuler, GD
中科院分区：
文献类型：
--
作者：
Rotmistrovsky, K;Jang, W;Schuler, GD
“电子 PCR”(e-PCR) 是指用于搜索 DNA 序列中序列标记位点 (STS) 的计算程序，每个标记位点由一对引物序列和预期 PCR 产物大小定义。为了提高速度，我们的实现从每个引物的 3' 端提取短“单词”，并将它们存储在可在搜索过程中有效访问的排序哈希表中。最近的一项改进是使用重叠的不连续单词来允许在存在不匹配的情况下找到匹配项。此外，在引物和序列之间的比对中可以允许存在间隙。这些变化的作用是提高灵敏度而不显着影响特异性。新软件提供了一种使用针对序列数据库的查询STS的搜索模式，以增强之前使用针对STS数据库的查询序列的可用模式。最后，e-PCR 现在可以通过网络服务使用，搜索结果链接到其他网络资源，例如 UniSTS 数据库和 MapViewer 基因组浏览器。 e-PCR 网络服务器可在 www.ncbi.nlm.nih.gov/sutils/e-pcr 上找到。
'Electronic PCR' (e-PCR) refers to a computational procedure that is used to search DNA sequences for sequence tagged sites (STSs), each of which is defined by a pair of primer sequences and an expected PCR product size. To gain speed, our implementation extracts short 'words' from the 3' end of each primer and stores them in a sorted hash table that can be accessed efficiently during the search. One recent improvement is the use of overlapping discontinuous words to allow matches to be found despite the presence of a mismatch. Moreover, it is possible to allow gaps in the alignment between the primer and the sequence. The effect of these changes is to improve sensitivity without significantly affecting specificity. The new software provides a search mode using a query STS against a sequence database to augment the previously available mode using a query sequence against an STS database. Finally, e-PCR may now be used through a web service, with search results linked to other web resources such as the UniSTS database and the MapViewer genome browser. The e-PCR web server may be found at www.ncbi.nlm.nih.gov/sutils/e-pcr.