Gene Myers and Susan Larson
Department of Computer Science, University of Arizona, Tucson, AZ 85721
We have completed the design and begun construction of a software environment in support of DNA sequencing called the "FAKtory". The environment consists of (1) our previously described software library, FAK, for the core combinatorial problem of assembling fragments, (2) a Tcl/Tk based interface, and (3) a software suite supporting a modest database of fragments and a processing pipeline that includes clipping and vector prescreening modules. A key feature of our system 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. Such customization need only be established once at a given location, subsequently users see a relatively simple system tailored to their needs. Indeed one may direct the system to input a raw dataset of say ABI trace files, pass them through a customized pipeline, and view the resulting assembly with two button clicks.
The system is built on top of our FAK software library and as a consequence one receives (a) high-sensitivity overlap detection, (b) correct resolution to large high-fidelity repeats, (c) near perfect multi-alignments, and (d) support of constraints that must be satisfied by the resulting assemblies. The FAKtory assumes a processing pipeline for fragments that consists of an INPUT phase, any number and sequence of CLIP, PRESCREEN, and TAG phases, followed by an OVERLAP and then an ASSEMBLY phase. The sequence of clip, prescreen, and tag phases is customizable and every phase is controlled by a panel of user-settable preferences each of which permits setting the phase's mode to AUTO, SUPERVISED, or MANUAL. This setting determines the level of interaction required by the user when the phase is run, ranging from none to hands-on. Any diagnostic situations detected during pipeline processing are organized into a log that permits one to confirm, correct, or undo decisions that might have been made automatically.
The customized fragment database contains fields whose type may be chosen from TIME, TEXT, NUMBER, and WAVEFORM. One can associate default values for fields unspecified on input and specify a control vocabulary limiting the range of acceptable values for a given field (e.g., John, Joe, or Mary for the field Technician, and [1, 36] for the field Lane). This database may be queried with SQL-like predicates that further permit approximate matching over text fields. Common queries and/or sets of fragments selected by them may be named and referred to later by said name. The pipeline status of a fragment may be part of a query.
The system permits one to maintain a collection of alternative assemblies, to compare them to see how they are different, and directly manipulate assemblies in a fashion consistent with sequence overlaps. The system can be customized so that a priori constraints reflecting a given sequencing protocol (e.g. double-barreled or transposon-mapped) are automatically produced according to the syntax of the names of fragments (e.g. X.f and X.r for any X are mates for double-barreled sequencing). The system presents visualizations of the constraints applied to an assembly, and one may experiment with an assembly by adding and/or removing constraints. Finally, one may edit the mutli-alignment of an assembly while consulting the raw waveforms. Special attention was given to optimizing the ergonomics of this time-intensive task.
*Supported by DOE grant DE-FG03-94ER61911.
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