Variation between observed and true Terminal Restriction Fragment length is dependent on true TRF length and purine content

Terminal Restriction Fragment (TRF) pattern analysis has become a widely used and informative tool for studying microbial communities. Variation between sequence-determined or true TRF length and observed TRF length (TRF drift) has been previously reported and can significantly affect identification...

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Bibliographic Details
Published in:Journal of microbiological methods 2003-07, Vol.54 (1), p.121-125
Main Authors: Kaplan, Christopher W, Kitts, Christopher L
Format: Article
Language:English
Subjects:
Bacteria - classification
Bacteria - genetics
Biological and medical sciences
DNA, Bacterial - analysis
DNA, Ribosomal - analysis
DNA, Ribosomal - genetics
Fundamental and applied biological sciences. Psychology
Genetic Variation
Microbiology
Polymorphism, Restriction Fragment Length
Purines - chemistry
RNA, Ribosomal, 16S - genetics
Sequence Analysis, DNA
Software
T-RFLP
TRF
TRFLP
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Summary:Terminal Restriction Fragment (TRF) pattern analysis has become a widely used and informative tool for studying microbial communities. Variation between sequence-determined or true TRF length and observed TRF length (TRF drift) has been previously reported and can significantly affect identification of bacterial species using TRF lengths predicted from sequence databases. In this study TRF drift was determined for 21 bacterial species using an ABI 310 Genetic Analyzer. TRF drift was positively correlated with true TRF length and negatively correlated with TRF purine content. This implies that subtle differences in molecular weight, whether from purine content or dye label, can significantly affect the observed TRF length.
ISSN:0167-7012
1872-8359
DOI:10.1016/S0167-7012(03)00003-4