Sequence type analysis and recombinational tests (START)
| Autor: | Martin C. J. Maiden, Man-Suen Chan, Keith A. Jolley, Edward J. Feil |
|---|---|
| Rok vydání: | 2001 |
| Předmět: |
Recombination
Genetic Statistics and Probability Genetics Lineage (genetic) Nucleic acid sequence Computational biology Biology Biochemistry Computer Science Applications Housekeeping gene Computational Mathematics Computational Theory and Mathematics DNA profiling Genes Bacterial Multilocus sequence typing Typing Databases Nucleic Acid Sequence Analysis Molecular Biology Software Selection (genetic algorithm) Sequence (medicine) |
| Zdroj: | Bioinformatics. 17:1230-1231 |
| ISSN: | 1367-4811 1367-4803 |
| DOI: | 10.1093/bioinformatics/17.12.1230 |
| Popis: | Summary: The 32-bit Windows application START is implemented using Visual Basic and C ++ and performs analyses to aid in the investigation of bacterial population structure using multilocus sequence data. These analyses include data summary, lineage assignment, and tests for recombination and selection. Availability: START is available at http://outbreak.ceid.ox. ac.uk/software.htm. Contact: keith.jolley@ceid.ox.ac.uk Multilocus Sequence Typing (MLST) is a nucleotide sequence-based typing method that indexes the variation present in bacterial housekeeping genes, where most of the variation is selectively neutral (Maiden et al., 1998). Internal fragments of seven housekeeping genes, approximately 450–500 bp in length, are sequenced and novel alleles are assigned with arbitrary numbers sequentially to provide an allelic profile of seven integers that defines the Sequence Type (ST) of each isolate. The technique is designed primarily for global or long-term epidemiology and surveillance, and has the advantage over other typing methods, such as genetic fingerprinting, of electronic portability and unambiguous characterization of isolates. MLST schemes have been developed for a range of bacterial pathogens and databases for these organisms can be interrogated at the MLST web-site (http://www.mlst.net/) thus facilitating rapid comparisons of isolates typed using the method. A further advantage of MLST is that it provides large quantities of data that may be analyzed by a number of evolutionary approaches to yield insights into the structure of bacterial populations and the selective pressures which act upon them. With the increasing availability of MLST data, the need for software to describe and analyze datasets has become apparent. Sequence Type Analysis and Recombinational Tests (START) was written to address this need through the inclusion of multiple analytical techniques in an easyto-use and intuitive interface for Windows 95/98/NT/2000 operating systems. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
|