Randomized algorithms, once viewed as a tool in computational number theory, have by now found widespread application. Growth has been fueled by the two major benefits of randomization: simplicity and speed. For many applications a randomized algorithm is the fastest algorithm available

ABSTRACT The BLAST programs are widely used tools for searching protein and DNA databases for sequence similarities. For protein comparisons, a variety of definitional, algorithmic and statistical refinements described here permits the execution time of the BLAST programs to be decreased

. An overview of basic concepts of information consensus in networks and methods of convergence and performance analysis for the algorithms are provided. Our analysis framework is based on tools from matrix theory, algebraic graph theory, and control theory. We discuss the connections between consensus problems

Emerging high-performance applications require the ability to exploit diverse, geographically distributed resources. These applications use high-speed networks to integrate supercomputers, large databases, archival storage devices, advanced visualization devices, and/or scientific instruments

.e. algebraic connectivity of the network) and the negotiation speed (or performance) of the corresponding agreement protocol. It turns out that balanced digraphs play an important role in addressing average-consensus problems. We introduce disagreement functions that play the role of Lyapunov functions

A tandem repeat in DNA is two or more contiguous, approximate copies of a pattern of nucleotides. Tandem repeats have been shown to cause human disease, may play a variety of regulatory and evolutionary roles and are important laboratory and analytic tools. Extensive knowledge about pattern size

HMMs. We present a method for detecting distant homologous relationships between proteins based on this approach. The method (HHsearch) is benchmarked together with BLAST, PSI-BLAST, HMMER, and the profile-profile comparison tools PROF_SIM and COMPASS, in an all-against-all compari-son of a database

. The combination of these two methods reveals a tool which is far simpler than a GA, and which out-performs a GA on large set of optimization problems in terms of both speed and accuracy. This paper presents an empirical analysis of where the proposed technique will outperform genetic algorithms, and describes a

and hierarchical memory. We discuss several important paradigms for how to solve batched and online problems efficiently in external memory. Programming tools and environments are available for simplifying the programming task. The TPIE system (Transparent Parallel I/O programming Environment) is both easy to use

ABSTRACT This paper investigates the effect of various tool speed combinations on the torque-tension relationship in a two-stage torque control process for the tightening of threaded fasteners. The tightening speed has a considerable affect on the thread and bearing friction coefficients. Hence