鉴定病毒及细菌的新方法－PLoS Comput Biol

细菌及病毒一直以来都是威胁人类最大的病源，而近年来这个威胁更是有增无减，只要有相关的病源菌DNA序列，利用已译码的基因组快速分析病源菌的种类，已经不再是是梦想。目前已有数百种的细菌及病毒的基因组（genome）序列被解开，可藉由这些DNA序列的分析快速判别各种微生物，美国马里兰大学的Adam Phillippy教授开发一个计算机程序，名为Insignia，可以经由细菌或病毒特有的DNA来识别各种已解碼的微生物。
研究人员表示Insignia是使用高效率的算法，将已知的病毒或细菌的基因组进行比对，然后再将这些比对结果贮存于数据库。这个程序也具有广泛的应用性，从诊断人类是否遭受感染到检验水系统的病菌等，都派得上用场。到目前为止，Insignia已成功的分析46种弧菌属的细菌，并刊登于5月份的PLoS Computational Biology期刊。更多关于Insignia的相关信息可参考以下网址：http://insignia.cbcb.umd.edu。
  
 
原始出处:
PLoS Comput Biol. 2007 May; 3(5): e98.
Published online 2007 May 18. Prepublished online 2007 April 18. doi: 10.1371/journal.pcbi.0030098.
Comprehensive DNA Signature Discovery and Validation
Adam M Phillippy,1* Jacquline A Mason,2 Kunmi Ayanbule,1 Daniel D Sommer,1 Elisa Taviani,3 Anwar Huq,3 Rita R Colwell,1,2 Ivor T Knight,1,2 and Steven L Salzberg1
1 Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America
2 Canon U.S. Life Sciences, Rockville, Maryland, United States of America
3 Center of Marine Biotechnology, University of Maryland Biotechnology Institute, Baltimore, Maryland, United States of America
 
* To whom correspondence should be addressed. E-mail: amp@umiacs.umd.edu
Received February 5, 2007; Accepted April 18, 2007.
 
Abstract
DNA signatures are nucleotide sequences that can be used to detect the presence of an organism and to distinguish that organism from all other species. Here we describe Insignia, a new, comprehensive system for the rapid identification of signatures in the genomes of bacteria and viruses. With the availability of hundreds of complete bacterial and viral genome sequences, it is now possible to use computational methods to identify signature sequences in all of these species, and to use these signatures as the basis for diagnostic assays to detect and genotype microbes in both environmental and clinical samples. The success of such assays critically depends on the methods used to identify signatures that properly differentiate between the target genomes and the sample background. We have used Insignia to compute accurate signatures for most bacterial genomes and made them available through our Web site. A sample of these signatures has been successfully tested on a set of 46Vibrio choleraestrains, and the results indicate that the signatures are highly sensitive for detection as well as specific for discrimination between these strains and their near relatives. Our approach, whereby the entire genomic complement of organisms are compared to identify probe targets, is a promising method for diagnostic assay development, and it provides assay designers with the flexibility to choose probes from the most relevant genes or genomic regions. The Insignia system is freely accessible via a Web interface and has been released as open source software at:http://insignia.cbcb.umd.edu.
Author Summary
Now that the genome sequences of hundreds of bacteria and viruses are known, we can design tests that will rapidly detect the presence of these species based solely on their DNA. Such tests have a wide range of applications, from diagnosing infections to detecting harmful microbes in a water supply. These tests can detect a pathogen in a complex mixture of organic material by recognizing short, distinguishing sequences—called DNA signatures—that occur in the pathogen and not in any other species. We present Insignia, a new computational system that identifies DNA signatures of any length in bacterial and viral genomes. Insignia uses highly efficient algorithms to compare sequenced bacterial and viral genomes against each other and to additional background genomes including plants, animals, and human. These comparisons are stored in a database and used to rapidly compute signatures for any particular target species. To maximize its utility for the community, we have made Insignia available as free, open-source software and as a Web application. We have also validated 50 Insignia-designed assays on a panel of 46 strains of Vibrio cholerae, and our results show that the signatures are both sensitive and specific.