Searching the World-Wide-Web using nucleotide and peptide sequences

*Background:* No approaches have yet been developed to allow instant searching of the World-Wide-Web by just entering a string of sequence data. Though general search engines can be tuned to accept ‘processed’ queries, the burden of preparing such ‘search strings’ simply defeats the purpose of quickly locating highly relevant information. Unlike ‘sequence similarity’ searches that employ dedicated algorithms (like BLAST) to compare an input sequence from defined databases, a direct ‘sequence based’ search simply locates quick and relevant information about a blunt piece of nucleotide or peptide sequence. This approach is particularly invaluable to all biomedical researchers who would often like to enter a sequence and quickly locate any pertinent information before proceeding to carry out detailed sequence alignment. 

*Results:* Here, we describe the theory and implementation of a web-based front-end for a search engine, like Google, which accepts sequence fragments and interactively retrieves a collection of highly relevant links and documents, in real-time. e.g. flat files like patent records, privately hosted sequence documents and regular databases. 

*Conclusions:* The importance of this simple yet highly relevant tool will be evident when with a little bit of tweaking, the tool can be engineered to carry out searches on all kinds of hosted documents in the World-Wide-Web.

*Availability:* Instaseq is free web based service that can be accessed by visiting the following hyperlink on the WWW
http://instaseq.georgetown.edu 
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Online Network Optimization Problems

. We survey results on online versions of the standard network optimization problems, including the minimum spanning tree problem, the minimum Steiner tree problem, the weighted and unweighted matching problems, and the traveling salesman problem. The goal in these problems is to maintain, with minimal changes, a low cost subgraph of some type in a dynamically changing network. 1 Introduction In the early 1920's Otakar Bor uvka was asked by the Electric Power Company of Western Moravia (EPCWM) to assist in EPCWM's electrification of southern Moravia by solving from a mathematical standpoint the question of how to construct the most economical electric power network [9]. In 1926 Bor uvka initiated the study of network optimization problems, by publishing an efficient algorithm for constructing a minimum spanning tree of a fixed network [9]. Certainly since the 1920's the underlying collection of sites that require electrification in southern Moravia has changed frequently as new sites ..

Fault-Tolerant Real-Time Scheduling

We use competitive analysis to study how to best use redundancy to achieve faulttolerance in online real-time scheduling. We show that the optimal way to use spatial redundancy depends on a complex interaction of the benefits, execution times, release times, and latest start times of the jobs. We give a randomized online algorithm whose competitive ratio is O(log \Phi log \Delta log 2 n log m log log m ) for transient faults. Here n is the number of jobs, m is the number of processors, \Phi is the ratio of maximum value density of a job to the minimum value density of a job, and \Delta the ratio of the longest possible execution time to the shortest possible execution time. We show that this bound is close to optimal by giving an \Omega\Gamma log \Delta\Phi loglog m ( logm log log m ) 2 ) lower bound on the competitive ratio of any randomized algorithm. In the case of permanent faults, there is a randomized online algorithm that has a competitive ratio of O(log \Phi log \Delt..

Online Weighted Matching

We introduce and study online versions of weighted matching problems in metric spaces. We present a simple 2k \Gamma 1 competitive algorithm for online minimum weighted bipartite matching where 2k is the number of nodes. We show that this competitiveness is optimal. For online maximum matching, we prove that the greedy algorithm achieves an optimal competitive factor of 3. In contrast, we prove that the greedy algorithm performs exponentially poorly for online minimum matching. Key words. online algorithm, matching, weighted matching, competitiveness AMS(MOS) subject classifications. 68P05, 68Q25, 68R10, 68R05 1 Introduction The assignment problem, finding a bipartite matching of minimum weight, is one of the archetypical problems in algorithmic graph theory and in combinatorial optimization [2, 10]. We introduce a natural online version of this problem, which we call online min-matching. Let G be a complete bipartite graph with one bipartition designated as the server vertices, an..

Randomized Algorithms for Real-time Scheduling with Fault-tolerance

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Maximizing Job Completions Online

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Speed is as Powerful as Clairvoyance

We consider several well known nonclairvoyant scheduling problems, including the problem of minimizing the average response time, and best-effort firm real-time scheduling. It is known that there are no deterministic online algorithms for these problems with bounded (or even polylogarithmic in the number of jobs) competitive ratios. We show that moderately increasing the speed of the processor used by the nonclairvoyant scheduler effectively gives this scheduler the power of clairvoyance. Furthermore, we show that there exist online algorithms with bounded competitive ratios on all inputs that are not closely correlated with processor speed. 1 Introduction We consider several well known nonclairvoyant scheduling problems, including the problem of minimizing the average response time [13, 15], and besteffort firm real-time scheduling [1, 2, 3, 4, 8, 11, 12, 18]. (We postpone formally defining these problems until the next section.) In nonclairvoyant scheduling some relevant information..