Data Driven Sequence Assembly

This grant will improve the software for DNA sequencing by integrating the components of basecalling, sequence assembly and post-assembly analysis into an integrated software system. To test theperformance of the software configurations, data for known regions of E. coli will be resequenced fromthe original clones using a LI-Cor sequencing instrument. The data will be basecalled by neural net basedpattern recognition and assembled with a variety of multiple alignment methods. Algorithmic solutionswill be compared and evaluated relative to the goal of achieving an accurate final sequence with theminimum of editing by a human expert. Alleviating the need for sequence editing will present theopportunity for significant cost savings in genome projects and other research involving DNA sequencing.