Global optimal eBURST analysis of multilocus typing data using a graphic matroid approach |
| |
Authors: | Alexandre P Francisco Miguel Bugalho Mário Ramirez João A Carriço |
| |
Affiliation: | 1. Instituto de Engenharia de Sistemas e Computadores – ID em Lisboa, Rua Alves Redol 9, 1000-029, Lisboa, Portugal 2. Instituto Superior Técnico, Universidade Técnica de Lisboa, Av. Rovisco Pais, 1049-001, Lisboa, Portugal 3. Instituto de Microbiologia/Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028, Lisboa, Portugal
|
| |
Abstract: | Background Multilocus Sequence Typing (MLST) is a frequently used typing method for the analysis of the clonal relationships among strains of several clinically relevant microbial species. MLST is based on the sequence of housekeeping genes that result in each strain having a distinct numerical allelic profile, which is abbreviated to a unique identifier: the sequence type (ST). The relatedness between two strains can then be inferred by the differences between allelic profiles. For a more comprehensive analysis of the possible patterns of evolutionary descent, a set of rules were proposed and implemented in the eBURST algorithm. These rules allow the division of a data set into several clusters of related strains, dubbed clonal complexes, by implementing a simple model of clonal expansion and diversification. Within each clonal complex, the rules identify which links between STs correspond to the most probable pattern of descent. However, the eBURST algorithm is not globally optimized, which can result in links, within the clonal complexes, that violate the rules proposed. |
| |
Keywords: | |
本文献已被 SpringerLink 等数据库收录! |
|