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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)
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)
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)
Viral genomes often contain genes recently acquired from microbes. In some cases (for example, psbA) the proteins encoded by these genes have been shown to be important for viral replication. In this study, using a unique search strategy on the Global Ocean Survey (GOS) metagenomes in combination with marine virome and microbiome pyrosequencing-based(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)
A floorplan represents the relative relations between modules on an integrated circuit. Floorplans are commonly classified as slicing, mosaic, or general. Separable and Bax-ter permutations are classes of permutations that can be defined in terms of forbidden subsequences. It is known that the number of slicing floorplans equals the number of separable(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)