Increasing Consensus Accuracy in DNA Fragment Assemblies by Incorporating Fluorescent Trace Representations

Proceedings Of The Fifth International Conference On Intelligent Systems For Molecular Biology

Volume

Proceedings Of The Fifth International Conference On Intelligent Systems For Molecular Biology

Contents

We present a new method for determining the consensus sequence in DNA fragment assemblies. The new method, "Trace-Evidence," directly incorporates aligned ABI trace information into consensus calculations via our previously described representation, "Trace-Data Classifications." The new method extracts and sums evidence indicated by the representation to determine consensus calls. Using the "Trace-Evidence" method results in automatically produced consensus sequences that are more accurate and less ambiguous than those produced with standard majority-voting methods. Additionally, these improvements are achieved with less coverage than required by the standard methods--using "Trace-Evidence" and a coverage of only three, error rates are as low as those with a coverage of over ten sequences.