小中大整理一些验证引物的电子PCR [转自 丁香园论坛]
整理一些验证引物的电子PCR [转自 丁香园论坛]
一对引物是否好用，除了用软件设计时的条件限制以外，
还可以通过在线工具验证是否能顺利扩增。
下面我把电子PCR的一些网址总结如下，如果大家使用过程有什么心得，一定拿出来分享啊！！！
[1]最熟悉的UCSC的In-Silico PCR
cuturl('http://www.genome.ucsc.edu/cgi-bin/hgPcr')
用法：将上下游引物分别输入，可以选择物种，基因组，产物长度等，submit即可
[2]NCBI的ePCR: cuturl('http://www.ncbi.nlm.nih.gov/sutils/e-pcr/')
blastn验证：网站内有详解 cuturl('http://blast.ncbi.nlm.nih.gov/Blast.cgi')
Primer-blast:序列，引物均输入
[3]iPCR
cuturl('http://www.ch.embnet.org/software/iPCR_form.html')
[4]VPCR
cuturl('http://www.sci.muni.cz/cgi-bin/vpcr.cgi')
VPCR网址：cuturl('http://www.sci.muni.cz/cgi-bin/vpcr.cgi')
The polymerase chain reaction(PCR) stands among the keystone technologies for analysis of biological sequence data. PCR is used to amplify DNA, to generate many copies from as little as a single template. This is essential, for example, in processing forensic DNAsamples, pathogen detection in clinical or biothreat surveillance applications, and medical genotyping for diagnosis and treatment of disease. It is used in virtually every laboratory doing molecular, cellular, genetic, ecologic, forensic, or medical research. Despite its ubiquity, we lack the precise predictive capability that would enable detailed optimization of PCR reaction dynamics. We are developing Virtual PCR (vPCR) software, an in silico method to model the kinetic, thermodynamic, and biological processes of PCR reactions.
Project Goals：
The challenges that we plan to address using vPCR include:
1.computational optimization of signatures for pathogen detection,for a significant savings in cost and time over purely empirical assay optimization;
2.assessment of signatures for forensic discrimination of closely related sequences.
从上面的介绍，可以看出来，VPCR就是通过计算模拟，来判断一对引物从基因组上P出来的产物结果怎么样。以后从基因组扩增基因，设计完引物，应该先运行一下virtual PCR，看看会不会有杂带。virtual PCR 可以试试看，娱乐一下。
参考文献：Virtual Polymerase Chain Reaction.pdf
什么是iPCR？
Paste a DNA sequence, ID or AC (ex. U73445) and the two primers (ex. forward AAA[AT]AA and reverse AAAGGG), select the format, and the options and click the "Run iPCR" button. The primer syntax allows the square parenthesis ([]) to specify an alternative and the dot (.) to replace the N for any nucleotide. The degenerated code is not allowed.
注意：This tool is not a primer "finder", if you are looking for such a tool, go to the Primer3 web site.（这不是一款设计引物的工具！）
原来，iPCR也是一种virtual PCR（查看）。能够计算出你设计的引物与模板的匹配性如何，看会出现哪些杂带，帮助你判断和选择引物。总之，它不是设计引物的工具！还是很有趣的，过来试试看吧。
iPCR网址：cuturl('http://www.ch.embnet.org/software/iPCR_form.html')
