CODEHOP: Unique web-based technology for gene discovery

描述(由申请人提供)： 我们开发了一种基于共识-简并杂交寡核苷酸引物(CODEHOPs)的新技术来扩增远缘基因序列。与用于检测Silico中相关序列的基本局部序列比对工具(BLAST)不同，CODEHOP可以在所有生物的基因组内容中搜索相关序列，而不限于现有电子数据库中包含的相对较少的序列。CODEHOP是从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，用于聚合酶链式反应(PCR)扩增，以快速和特异地识别属于共同基因家族的远缘同源基因和同源基因。我们已经开发了预测CODEHOP的软件，并使其可以在WWW上免费访问。自问世以来，CODEHOP技术已被证明在识别未知病毒病原体以及识别与各种生物过程和疾病有关的病毒和细胞基因的结构特征方面具有极高的价值。CODEHOPS和相关软件目前正被越来越多从事不同模式生物和主题的科学家在世界范围内成功地使用。然而，从我们从CODEHOP用户那里收到的许多电子邮件中可以明显看出，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，我们的长期目标是为科学界提供一种用户友好、快速和可靠的技术，用于识别和比较广泛生物范围内的相关基因。这项应用的目标是进一步开发独特的CODEHOP技术，并通过识别和表征与癌症发病机制有关的新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的聚合酶链式反应技术，并将所有成果添加到现有的CODEHOP网站上。拟议项目的意义在于增加了这项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和生物医学重要性的基因。

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.