95. The FAKtory Sequence Assembly System 

Susan J. Miller, Eugene W. Myers, Kedarnath A. Dubhashi, and Daniel E. Garrison 
University of Arizona, Tucson, Arizona 
susanjo@cs.arizona.edu 

The FAKtory system facilitates sophisticated prescreening, assembly, contig layout manipulation and finishing for DNA sequencing projects. The system allows specialized database configuration, definition of operations performed on sequences, constraint-based assemblies, and convenient linking to post-assembly analysis software. Each user can configure various FAKtory displays and can select the degree of control desired over each of the operations. Retaining our original design goals of customizability and sound ergonomics, we have continued to add features to FAKtory. 

Among our recent additions to the system are allowing input of pre-trimmed sequence data and input of SCF format data. We have made a dramatic speed improvement and have increased the sensitivity of overlap detection in the underlying FAKII assembly kernel. A report generator has been added to FAKtory and we have developed a separate graphical viewer for comparing CAF or ace format assemblies. The finishing editor now has the capability of running the GENSCAN program and displaying any exons found in the six reading frames. Optionally, the consensus sequence can be filtered through the CENSOR or RepeatMasker programs before searching for exons. 

Currently under development are improved overlap detection using quality values and enhancements to the Finishing editor. In addition, fragment prescreening based on quality numbers will be incorporated into the system. We also plan to add the capability of importing GAF format assemblies into FAKtory and to integrate the graphical comparison tool for more convenient comparisons of alternate assemblies generated by FAKII or by other assemblers.