CODEHOP: Unique web-based technology for gene discovery

描述（由申请人提供）： 我们已经开发了一种新的技术来扩增基于共识简并杂交寡核苷酸引物（CODEHOPs）的远亲基因序列。与用于通过计算机检测相关序列的“基本局部序列比对工具”（BLAST）不同，CODEHOP可以在所有生物体的基因组内容中搜索相关序列，并且不限于现有电子数据库中包含的相对较少的序列。CODEHOP是从来自蛋白质家族成员的多重比对蛋白质序列的高度保守区域设计的，并且用于PCR扩增以快速且特异性地鉴定属于共同基因家族的远缘直系同源物和旁系同源物。我们开发了预测CODEHOPs的软件，并在WWW上免费提供。自成立以来，CODEHOP技术已被证明在鉴定未知病毒病原体以及鉴定与各种生物过程和疾病有关的病毒和细胞基因及其结构表征方面具有非常宝贵的价值。CODEHOPs和相关软件目前正在全世界范围内被越来越多的科学家成功地使用，他们研究的模式生物和主题各不相同。然而，从我们收到的许多CODEHOP用户的电子邮件来看，我们显然需要改进和扩大我们的技术范围。解决这些问题对于实现我们的长期目标至关重要，该目标是为科学界提供独特的用户友好，快速和可靠的技术，用于在广泛的生物体中识别和结构比较相关基因。本申请的目的是进一步开发独特的CODEHOP技术，并通过鉴定和表征与癌症发病机制有关的新型细胞基因和病毒病原体来验证改进和变化。我们的目标是进一步开发和改进CODEHOP软件和基于CODEHOP的PCR技术，并将所有结果添加到现有的CODEHOP网站。拟议项目的意义在于提高这一重要技术的用户友好性、速度和准确性。我们预计，这将导致加快发现与疾病有关的病原体以及具有生物学和生物医学重要性的基因的步伐。

DESCRIPTION (provided by applicant): We have developed a novel technology to amplify distantly related gene sequences based on consensus-degenerate hybrid oligonucleotide primers (CODEHOPs). Unlike the "Basic Local Sequence Alignment Tool (BLAST) used to detect related sequences in silico, CODEHOPs can search for related sequences in the genome content of all living organisms, and is not limited to the relatively few sequences contained within the existing electronic databases. CODEHOPs are designed from highly conserved regions of multiply aligned protein sequences from members of a protein family and are used in PCR amplification to rapidly and specifically identify distantly related orthologs and paralogs belonging to a common gene family. We have developed software to predict CODEHOPs and made it freely accessible on the WWW. Since its inception, the CODEHOP technology has proven invaluable for the identification of unknown viral pathogens as well as the identification and structural characterization of viral and cellular genes implicated in various biological processes and disease. CODEHOPs and the related software are currently being used successfully worldwide by an increasing number of scientists working on widely different model organisms and subjects. However, the need to improve and broaden the scope of our technology has become apparent from the many e-mails we have received from CODEHOP users. To address these issues is critical to achieve our long-term goal to uniquely provide the scientific community with a user-friendly, fast and reliable technology for the identification and structural comparison of related genes within a broad range of organisms. The objective of this application is to further develop the unique CODEHOP technology and validate improvements and changes by identifying and characterizing novel cellular genes and viral pathogens that are implicated in cancer pathogenesis. Our AIMS are to further develop and improve the CODEHOP software and CODEHOP-based PCR technology and add all outcomes to the existing CODEHOP web site. The significance of the proposed project lies in increasing the user-friendliness, speed and accuracy of this important technology. We expect that this will lead to an increased pace of discovery of pathogens implicated in disease, as well as genes of biological and biomedical importance.