Will Gillett

Genome sequence of Francisella Tularensis subspecies holarctica Strain FSC200, isolated from a child with Tularemia

Here we report the complete, accurate 1.89-Mb genome sequence of Francisella tularensis subsp. holarctica strain FSC200, isolated in 1998 in the Swedish municipality Ljusdal, which is in an area where tularemia is highly endemic. This genome is important because strain FSC200 has been extensively used for functional and genetic studies of Francisella and is well-characterized.

Fragment collapsing and splitting while assembling high-resolution restriction maps.

In the process of constructing high-resolution restriction maps via greedy algorithms, a classical anomaly, known as fragment collapsing, introduces errors into the maps that impedes further map assembly. Fragment collapsing occurs when two different genomic fragments of approximately the same length and occurring in the digestion of two different overlapping clones are incorrectly identified as representative of a single genomic fragment. This introduces a single fragment of commensurate length into an incorrect position in the map. The present work describes techniques for detecting and correcting such anomalies.

DNA Mapping Algorithms: Fragment Matching Mistake Detection and Correction

When using random clone overlap based methods to make DNA maps, fragment matching mistakes, the incorrect matching of similar length restriction fragments, are a common problem that produces incorrect maps. Previous work presented the Restricted Splitting Algorithm (or RSA), which is useful for repairing a map containing a fragment mistake when the location of the mistake is known. This work presents an algorithm, called FIX, which attempts to identify the location of the fragment matching mistake and then uses the RSA to repair the map containing the mistake. In essense, the two techniques combined constitute a hypothesis formulation/hypothesis verification... Read complete abstract on page 2.

DNA Mapping Algorithms: Synchronized Double Digest Mapping

A technique called Synchronized Double Digest Mapping (SDDM) is presented; it combines classical Double Digest Mapping (DDM) and Multiple-Restriction-Enzyme Mapping (MREM). Classical DDM is a technique for determining the order of restriction fragments in a clone given three digestions of the clone: a digestion by enzyme1, a digestion by enzyme2, and a digestion by enzyme1 and enzyme2 combined. All algorithms for applying this technique are exponential (in the number of fragments present in the clone) in nature. MREM is an extension of classical high-resolution restriction-fragment mapping of a YAC or a genome, in which the overlaps among a set... Read complete abstract on page 2.

DNA Mapping Algorithms: Abstract Data Types - Concepts and Implementation

The conceptual aspects of and the implementation details of a set of self-identifying abstract data types (ADT) are described. Each of the ADTs constitutes a specific class of object, upon which a set of well-defined access functions is available. The intent of these ADTs is to supply a paradigm in which a class of object is available for manipulation, but in which the underlying implementation is hidden from the application programmer. Specific ADTs are the described in some detail. The tagged architecture used to achieve the self-identifying property of the ADTs is presented, and a set of required system-backbone... Read complete abstract on page 2.

Embedding semantics in LR parser tables

This paper addresses two of the problems commonly associated with LR parsing and syntax directed translation schemes, namely grammar stratification and excessively large table size, A solution is discussed which can eliminate stratification of the grammar by allowing the designer to embed semantics directly within the LR table (i.e., at shift and error entries instead of just at reduce entries) and to use global context to determine what semantics should be performed. The non‐stratified grammar can produce a significantly smaller LR table than the corresponding stratified grammar. The compatibility of this scheme with commonly used table compaction techniques is also discussed.

On binary tree encodements

SummaryA data encoding scheme involving binary tree encodements is presented and analyzed. A closed-form formula for the number of n-bit legal memory configurations is developed. It is shown that the storage capacity loss due to the use of this scheme is not significant for large n.

ON FINDING TOPOLOGICALLY VALID MATCHINGS IN RESTRICTION-FRAGMENT MAPS

We examine a problem that arises in physical DNA mapping, namely determining what common DNA is represented in two maps. We present an example illustrating the properties of DNA mapping, and motivate our approach. We present a new graph structure, called the Ƶ-graph, that takes advantage of structure that develops during the mapping process, thus catalyzing the discovery of all relevant fragment matchings. We describe an algorithm based on this structure and present experimental data supporting its improved performance as compared with a naive approach.