Assembly as part of a DNA sequence management system

Zmasek, C. M.1, Lapp, H.2, Ching, K.; Wiltshire, T.; Fletcher, C.; Orth, A., Genomics Institute of the Novartis Research Foundation;, Genomics Institute of the Novartis Research Foundation

Controlling the DNA sequence assembly process through a command line interface is inconvenient and error prone. Therefore, we developed a system which allows the user to manage the assembly process through a graphical user interface. This system is part of our sequence management tool SEQTRACS. This gives it direct access to database stored sequence trace data. The system is organized around a central assembly server which performs the assembly using PHRED/PHRAP. The user interaction is through Java based thick clients. A particularly useful feature of this system is that it stores "assembly projects" in the database. Assembly projects contain all the relevant information of a particular assembly process (e.g. software parameters, input sequence information, output sequence information). This allows the user (for example) to perform incremental assemblies by adding new trace files to an existing assembly project or to assemble the same set of sequences using different software parameters with a minimum of inconvenience.