生物谷報道：細菌及病毒一直以來都是威脅人類最大的病源，而近年來這個威脅更是有增無減,，只要有相關(guān)的病源菌DNA序列，利用已譯碼的基因組快速分析病源菌的種類,，已經(jīng)不再是是夢想,。目前已有數(shù)百種的細菌及病毒的基因組（genome）序列被解開，可藉由這些DNA序列的分析快速判別各種微生物，美國馬里蘭大學(xué)的Adam Phillippy教授開發(fā)一個計算機程序,，名為Insignia,，可以經(jīng)由細菌或病毒特有的DNA來識別各種已解碼的微生物。
研究人員表示Insignia是使用高效率的算法,，將已知的病毒或細菌的基因組進行比對,，然后再將這些比對結(jié)果貯存于數(shù)據(jù)庫。這個程序也具有廣泛的應(yīng)用性,，從診斷人類是否遭受感染到檢驗水系統(tǒng)的病菌等,，都派得上用場。到目前為止,，Insignia已成功的分析46種弧菌屬的細菌,，并刊登于5月份的PLoS Computational Biology期刊。更多關(guān)于Insignia的相關(guān)信息可參考以下網(wǎng)址：http://insignia.cbcb.umd.edu,。
(資料來源 : Bio.com)
原始出處:
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: [email protected]
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 46 Vibrio cholerae strains, 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.
