论文信息 - A bioinformatics pipeline for high-throughput microbial multilocus sequence typing (MLST) analyses.

A bioinformatics pipeline for high-throughput microbial multilocus sequence typing (MLST) analyses.

Multilocus sequence typing (MLST) analysis for semi-routine applications is hindered by the downstream, manually intensive steps of processing the raw sequence data files. This report describes the development of an MLST pipeline that automates DNA sequence editing and analysis in order to significantly reduce the time required for processing data. Validation using a pneumococcal dataset revealed complete agreement between the results generated by manual and automated workflows. The MLST pipeline was developed for both double-strand and single-strand sequencing.

[1] Martin C. J. Maiden,et al. mlstdbNet – distributed multi-locus sequence typing (MLST) databases , 2004, BMC Bioinformatics.

[2] P Green,et al. Base-calling of automated sequencer traces using phred. II. Error probabilities. , 1998, Genome research.

[3] P. Green,et al. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. , 1998, Genome research.

[4] M. Achtman,et al. Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[5] B. Spratt,et al. A multilocus sequence typing scheme for Streptococcus pneumoniae: identification of clones associated with serious invasive disease. , 1998, Microbiology.

[6] M. Enright,et al. Molecular Typing of Bacteria Directly from Cerebrospinal Fluid , 2000, European Journal of Clinical Microbiology and Infectious Diseases.

[7] R. George,et al. Multilocus Sequence Typing Directly on DNA from Clinical Samples and a Cultured Isolate To Investigate Linked Fatal Pneumococcal Disease in Residents of a Shelter for Homeless Men , 2005, Journal of Clinical Microbiology.

[8] Martin C. J. Maiden,et al. Database-driven Multi Locus Sequence Typing (MLST) of bacterial pathogens , 2001, Bioinform..

[9] David M. Aanensen,et al. The multilocus sequence typing network: mlst.net , 2005, Nucleic Acids Res..