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MOTIVATION Several genome-scale efforts are underway to reconstruct metabolic networks for a variety of organisms. As the resulting data accumulates, the need for analysis tools increases. A notable requirement is a pathway alignment finder that enables both the detection of conserved metabolic pathways among different species as well as divergent metabolic(More)
Cyanobacteria of the Synechococcus and Prochlorococcus genera are important contributors to photosynthetic productivity in the open oceans. Recently, core photosystem II (PSII) genes were identified in cyanophages and proposed to function in photosynthesis and in increasing viral fitness by supplementing the host production of these proteins. Here we show(More)
Genes and proteins generate molecular circuitry that enables the cell to process information and respond to stimuli. A major challenge is to identify characteristic patterns in this network of interactions that may shed light on basic cellular mechanisms. Previous studies have analyzed aspects of this network, concentrating on either(More)
Global register allocation and spilling is commonly performed by solving a graph coloring problem. In this paper we present a new coherent set of heuristic methods for reducing the amount of spill code generated. This results in more efficient (and shorter) compiled code. Our approach has been compared to both standard and priority-based coloring(More)
Many problems that arise in general channel routing manifest themselves in simpler situations. We consider connecting a set of n terminals on a line to another set on a parallel line across a rectangular channel. We show that in any solution to the problem that (almost) minimizes the width of the channel (i.e. the distance between the lines the terminals(More)
We introduce a generalization of interval graphs, which we call <i>dotted interval graphs (DIG).</i> A dotted interval graph is an intersection graph of arithmetic progressions (=<i>dotted intervals</i>). Coloring of dotted intervals graphs naturally arises in the context of high throughput genotyping. We study the properties of dotted interval graphs, with(More)
We consider the problem of sorting linear and circular permutations and 0/1 sequences by reversals in a length-sensitive cost model. We extend the results on sorting by length-weighted reversals in two directions: we consider the signed case for linear sequences and also the signed and unsigned cases for circular sequences. We give lower and upper bounds as(More)
The optimal transformation of one tree into another by means of elementary edit operations is an important algorithmic problem that has several interesting applications to computational biology. Here we introduce a constrained form of this problem in which a partial mapping of a set of nodes (the " seeds ") in one tree to a corresponding set of nodes in the(More)
We study the problem of sorting binary sequences and permutations by length-weighted reversals. We consider a wide class of cost functions, namely f () = α for all α ≥ 0, where is the length of the reversed subsequence. We present tight or nearly tight upper and lower bounds on the worst-case cost of sorting by reversals. Then we develop algorithms to(More)
We study the classic Graph Motif problem: given a graph G = (V, E) with a set of colors for each node, and a multiset M of colors, we seek a subtree T ⊆ G, and a coloring of the nodes in T , such that T carries exactly (also with respect to multiplicity) the colors in M. Graph Motif plays a central role in the study of pattern matching problems, primarily(More)