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SUMMARY Tandem Repeat Occurrence Locator (TROLL), is a light-weight Simple Sequence Repeat (SSR) finder based on a slight modification of the Aho-Corasick algorithm. It is fast and only requires a standard Personal Computer (PC) to operate. We report running times of 127 s to find all SSRs of length 20 bp or more on the complete Arabdopsis genome--approx.(More)
Existing memory models and cache consistency protocols assume the memory coherence property which requires that all processors observe the same ordering of write operations to the same location. In this paper, we address the problem of de ning a memory model that does not rely on the memory coherence assumption, and also the problem of designing a cache(More)
MOTIVATION Knowledge of the transmembrane helical topology can help identify binding sites and infer functions for membrane proteins. However, because membrane proteins are hard to solubilize and purify, only a very small amount of membrane proteins have structure and topology experimentally determined. This has motivated various computational methods for(More)
In this paper, we propose the use of cyclic interval graphs as an alternative representation for register allocation. The \thickness" of the cyclic interval graph captures the notion of overlap between live ranges of variables relative to each particular point of time in the program execution. We demonstrate that cyclic interval graphs provide a feasible(More)
In this paper we address the following software pipelining problem: given a loop and a machine architecture with a fixed number of processor resources (e.g. function units), how can one construct a software-pipelined schedule which runs on the given architecture at the maximum possible iteration rate (a&grave; la <bold>rate-optimal</bold>) while minimizing(More)
Loop identification is a necessary step in loop transformations for high-performance architectures. One classical technique for detecting loops is Tarjan's interval-finding algorithm. The intervals identified by Tarjan's method are single-entry, strongly connected subgraphs that closely reflect a program's loop structure. We present a simple algorithm for(More)
Parallel systems supporting multithreading, or message passing in general, have typically used either polling or interrupts to handle incoming messages. Neither approach is ideal; either may lead to excessive overheads or message-handling latencies, depending on the application. This paper investigates a combined approach---<i>Polling Watchdog,</i> where(More)
Many attempts have been made to add concurrency to C ++ , but much of the work has not exploited the power of C ++ , and often extensive compiler extensions are made. This paper shows how the object-oriented facilities of C ++ are powerful enough to encapsulate concurrency creation and control. We have developed a concurrent C ++-based system which we call(More)