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Chapter 44 : Development of an Online Tool for European Working Group for Infections Sequence-Based Typing, Including Automatic Quality Assessment and Data Submission

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Development of an Online Tool for European Working Group for Infections Sequence-Based Typing, Including Automatic Quality Assessment and Data Submission, Page 1 of 2

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Abstract:

Assessment of the sequence quality is a skilled task and can often be very subjective. Therefore, the primary aim of the study described in this paper was to develop novel web-based tools to facilitate: (i) database curation, designation of novel allele types, and allelic profiles; (ii) automated quality assessment of sequence chromatograms. The outcome of the study is an online tool, which is now accessible via the European Working Group for Legionella infections website to allow users to assemble sequence traces (from the sequence-based typing (SBT) scheme) and to identify matching preexisting alleles. Most SBT types are derived from at least two sequences, typically one forward and one reverse sequence. Extensive sequence analysis and manipulation of the sequences and assembled contig is carried out using the BioPerl toolkit of objects. The processes involved include quality-trimming, assessment of the proportion of the contig that is double-stranded, and consensus generation. Data analysis from multicenter proficiency SBT analysis has confirmed that misidentification readily occurs when poor-quality trace files are used. This online tool will help systemically check sequence quality and will assist in the determination of minimum standards for a range of sequence quality parameters, ensuring that only high-quality data is accepted for allele and profile identification.

Citation: P. Underwood A, Bellamy W, Afshar B, K. Fry N, G. Harrison T. 2006. Development of an Online Tool for European Working Group for Infections Sequence-Based Typing, Including Automatic Quality Assessment and Data Submission, p 163-166. In Cianciotto N, Kwaik Y, Edelstein P, Fields B, Geary D, Harrison T, Joseph C, Ratcliff R, Stout J, Swanson M (ed), . ASM Press, Washington, DC. doi: 10.1128/9781555815660.ch44

Key Concept Ranking

Legionella pneumophila
0.8125
Sequence Analysis
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0.8125
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Figures

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FIGURE 1

The output displayed on the web page after uploading and processing two trace files from one locus of the SBT typing scheme with the sequence quality tool.

Citation: P. Underwood A, Bellamy W, Afshar B, K. Fry N, G. Harrison T. 2006. Development of an Online Tool for European Working Group for Infections Sequence-Based Typing, Including Automatic Quality Assessment and Data Submission, p 163-166. In Cianciotto N, Kwaik Y, Edelstein P, Fields B, Geary D, Harrison T, Joseph C, Ratcliff R, Stout J, Swanson M (ed), . ASM Press, Washington, DC. doi: 10.1128/9781555815660.ch44
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References

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