iCODEHOP: a new interactive program for designing COnsensus-DEgenerate Hybrid Oligonucleotide Primers from multiply aligned protein sequences.
iCODEHOP: a new interactive program for designing COnsensus-DEgenerate Hybrid Oligonucleotide Primers from multiply aligned protein sequences.
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DOI：
10.1093/nar/gkp379
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发表时间：
2009-07
影响因子：
14.9
通讯作者：
Rose TM
中科院分区：
文献类型：
--
作者：
Boyce R;Chilana P;Rose TM
使用COnsensus简并杂交寡核苷酸引物（CODEHOPs）的PCR扩增已被证明对于鉴定未知病原体和表征新基因非常有效。我们描述iCODEHOP;一个新的交互式网络应用程序，简化了设计和选择从多重比对蛋白质序列的CODEHOPs的过程。iCODEHOP智能地指导用户完成简并引物设计过程，包括上传序列、创建多重比对、推导CODEHOP和计算其退火温度。用户可以快速扫描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子分支中轻松设计新的引物。它还允许用户使用序列权重使引物设计偏向于特定进化枝或序列。所有感兴趣的研究人员都可以在https://icodehop.cphi.washington.edu/i-codehop-context/Welcome上免费获得iCODEHOP。
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.
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影响因子：
3
作者：
Lamprecht AL;Margaria T;Steffen B;Sczyrba A;Hartmeier S;Giegerich R
通讯作者：
Giegerich R
影响因子：
14.9
作者：
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通讯作者：
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影响因子：
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通讯作者：
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影响因子：
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作者：
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通讯作者：
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