CODEHOP: Unique web-based technology for gene discovery

CODEHOP：独特的基于网络的基因发现技术

基本信息

批准号：
7919902
负责人：
TIMOTHY M ROSE
金额：
$ 30.21万
依托单位：
SEATTLE CHILDREN'S HOSPITAL
依托单位国家：
美国
项目类别：
财政年份：
2009
资助国家：
美国
起止时间：
2009-09-24 至 2011-09-23
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/7919902
关键词：
CODEHOP Unique web based technology

项目摘要

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.

描述（由申请人提供）：我们已经开发了一种新型技术，可以基于共有排定的混合寡核苷酸引物（CodeHops）扩大相关的基因序列。 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属于一个共同基因家族的直系同源物和旁系同源物可以在www上自由访问，并在www上自由访问。越来越多的科学家从事广泛不同的模型生物和受试者。但是，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，改善和扩大技术范围的需求已变得显而易见。解决这些问题对于实现我们的长期目标至关重要，以便为科学界提供一种用户友好，快速和可靠的技术，以识别和结构性比较广泛的生物体内的相关基因。该应用的目的是通过识别和表征与癌症发病机理有关的新型细胞基因和病毒病原体来进一步开发独特的Codehop技术，并通过识别和表征新颖的细胞基因和病毒病原体来验证改善和变化。我们的目的是进一步开发和改进基于CodeHop的PCR技术，并将所有结果添加到现有的Codehop网站。拟议项目的重要性在于提高这项重要技术的用户友好性，速度和准确性。我们预计，这将导致发现与疾病有关的病原体以及生物学和生物医学重要性的基因的提高。