The University of Arizona, Computer Science Department
Current Research Projects

FAKtory: A software environment for DNA Sequencing
We have built a prototype software environment in support of DNA sequencing called ``FAKtory''. The environment consists of (1) our software library, FAK II, for the core combinatorial problem of assembling fragments, (2) a Tcl/Tk based interface, and (3) a software suite supporting a database of fragments and a processing pipeline that includes clipping, tagging, and vector removal modules. A key feature of FAKtory is that it is highly customizable: the structure of the fragment database, the processing pipeline, and the operation of each phase of the pipeline are specifiable by the user. Yet such customization need only be established once at a given site, subsequently users see a relatively simple system tailored to their needs.


FAKtory Overview (html)
FAK II Interface Doc. (postscript)
Unix Toolkit for FAK II (postscript)


Gene Myers (P.I., Professor)
Susan Miller (Systems Programmer)
Eric Anson (Ph.D. Candidate, FAKII)