an algorithm for mapping positively selected members of quasispecies-type viruses一个算法映射积极选择quasispecies-type病毒的成员.pdfVIP

BMC Bioinformatics (2001) 2:1 /1471-2105/2/1 BMC Bioinformatics (2001) 2:1 Research article An algorithm for mapping positively selected members of quasispecies-type viruses 1 2,3 2 Jeffrey J Stewart* , Perry Watts and Samuel Litwin Address: 1BioGenetic Ventures, 1100 Olive Way, Suite 300, Seattle, WA 98101, 2Fox Chase Cancer Center, Institute for Cancer Research, 7701 Burholme Avenue, Philadelphia, PA 19111 and 3IMS Health, 660 West Germantown Pike, Plymouth Meeting, PA 19462-1048 E-mail: Jeffrey J Stewart* - jjs@; Perry Watts - wattsp@; Samuel Litwin - litwin@ *Corresponding author Published: 6 March 2001 Received: 12 June 2000 Accepted: 6 March 2001 BMC Bioinformatics 2001, 2:1 This article is available from: /1471-2105/2/1 (c) 2001 Stewart et al, licensee BioMed Central Ltd. Abstract Background: Many RNA viruses do not have a single, representative genome but instead form a set of related variants that has been called a quasispecies. The sequence variability of such viruses presents a significant bioinformatics challenge. In order for the sequence information to be understood, the complete mutational spectrum needs to be distilled to a biologically relevant and analyzable representation. Results: Here, we develop a selection mapping algorithm--QUASI--that identifies the positively selected variants of viral proteins. The key to the selection mapping algorithm is the identification of particular replacement mutations that are overabundant relative to silent mutations at