Open AccessFinal Report: A Flexible Sequency Reconstructor for Large-Scale DNA Sequencing Projects, September 1, 1994 - August 31, 1999
Author(s) -
Susan J. Miller,
Gene Myers
Publication year - 1999
Language(s) - English
Resource type - Reports
DOI - 10.2172/765731
Subject(s) - computer science , compatibility (geochemistry) , joins , file format , backward compatibility , directory , interfacing , testbed , data file , file system , software , database , software engineering , operating system , world wide web , computer hardware , programming language , engineering , chemical engineering
Because no current assembly system produces perfect results on all data, some users prefer to use FAKtory in tandem with other assembly systems, and compare the results to help identify false joins or chimeric sequences. Our gryphon tool can aid in this process by displaying a graphical view of a FAKtory assembly alongside any other format assembly. One of our goals has been to allow interfacing between different systems, and as a result of these efforts, the FAKII kernel is the preferred assembly engine of many GAP4 users worldwide. Recent developments of the FAKtory project has focused on enhancing output capabilities to increase compatibility with other tools, improving the performance and increasing the robustness of the system, and adding features based on user requests. FAKtory can now output entire assemblies in FASTA format, and can product PostScript file captures of the Layout, MultiAlignment and Trace views. For compatibility with the GAP4 system, the FAKII Overlap Graph and Assembly objects can now be saved from FAKtory. As an aid to project organization, input and output are automatically directed to a specified project directory which is selectable via a File Selection Box incorporated into the File Directories panel. A File Selection Box is also provided when an output operation is initiated to allow easy redirection of output