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- W2433808512 abstract "The relative separations and yields of oligomers DNA sequencing ladders are informative complements to the traditional determinants of base sequence identification. In Sanger sequencing ladders, oligomer yield variance reflects the influence of local template DNA sequence on the velocity of ddNTP incorporation by DNA polymerase during chain elongation/termination. Patterns of oligomer yields represented in ladder images are DNA polymerase-specific under similar reaction conditions. These patterns are consistent among results generated with different sequencing instruments.We have developed a signal conditioning and basecalling processor, incorporating artificial neural networks, for analysis of sequencing ladder images of products from fluorescence-labelled sequencing reactions. The processor generates feature tables reporting measured values of separations and yields for each detected oligomer. A contextual analysis of the patterns of oligomers yield generated by two DNA polymerases, the thermophilic polymeraseTaq and the exo-polymerase T7 (Sequenase), reveals behaviors unique to each.The analysis of oligomer yield variance helps to define energetics of DNA polymerase interactions with specific DNA sequences of interest, such as mutational hot spots. I have demonstrated the influence of base stacking interactions to be a major contributor to the yield variance in sequencing ladders generated by T7 (Sequenase). In contrast, there is no such influence of base stacking interactions on nucleotide insertion kinetics of the Taq DNA polymerase.The contextual analysis of oligomer yield and separation variance has been incorporated into a pattern recognition-based editor for improved accuracy of basecalling with automated, high-throughput DNA sequencers." @default.
- W2433808512 created "2016-06-24" @default.
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- W2433808512 date "1995-11-20" @default.
- W2433808512 modified "2023-09-24" @default.
- W2433808512 title "Oligomer yields in DNA sequencing ladders" @default.
- W2433808512 hasPublicationYear "1995" @default.
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