Boyce Richard, Chilana Parmit, Rose Timothy M
Department of Biomedical Informatics, University of Pittsburgh, UPMC Cancer Pavilion, Suite 301, Pittsburgh, PA 15232, USA.
Nucleic Acids Res. 2009 Jul;37(Web Server issue):W222-8. doi: 10.1093/nar/gkp379. Epub 2009 May 14.
PCR amplification using COnsensus DEgenerate Hybrid Oligonucleotide Primers (CODEHOPs) has proven to be highly effective for identifying unknown pathogens and characterizing novel genes. We describe iCODEHOP; a new interactive web application that simplifies the process of designing and selecting CODEHOPs from multiply-aligned protein sequences. iCODEHOP intelligently guides the user through the degenerate primer design process including uploading sequences, creating a multiple alignment, deriving CODEHOPs and calculating their annealing temperatures. The user can quickly scan over an entire set of degenerate primers designed by the program to assess their relative quality and select individual primers for further analysis. The program displays phylogenetic information for input sequences and allows the user to easily design new primers from selected sequence sub-clades. It also allows the user to bias primer design to favor specific clades or sequences using sequence weights. iCODEHOP is freely available to all interested researchers at https://icodehop.cphi.washington.edu/i-codehop-context/Welcome.
使用简并共有杂交寡核苷酸引物（CODEHOPs）进行PCR扩增已被证明在鉴定未知病原体和表征新基因方面非常有效。我们描述了iCODEHOP；这是一个新的交互式网络应用程序，它简化了从多重比对的蛋白质序列中设计和选择CODEHOPs的过程。iCODEHOP通过简并引物设计过程智能地引导用户，包括上传序列、创建多重比对、推导CODEHOPs并计算其退火温度。用户可以快速浏览程序设计的一整套简并引物，以评估其相对质量，并选择单个引物进行进一步分析。该程序显示输入序列的系统发育信息，并允许用户从选定的序列亚分支轻松设计新引物。它还允许用户使用序列权重使引物设计偏向于特定的分支或序列。所有感兴趣的研究人员均可在https://icodehop.cphi.washington.edu/i-codehop-context/Welcome免费使用iCODEHOP。
