A COMPARISON OF TWO DNA SEQUENCING METHODS

In the paper the problem of DNA sequencing is considered. The sequencing methodby Pevzner [8] is analyzed and its generalization, allowing for finding all acceptablesolutions, is described. It is then compared with another method based on a generation of asolution tree [4],keywords: DNA sequencing, hybridization method, complexity analysis.Pozna

SUBOPTIMAL APPROACHES TO SCHEDULING MALLEABLE TASKS

In the paper, the problem of scheduling a set of n malleable tasks on m parallel computers is considered. The tasks may be executed by several processors simultaneously and the processing speed of a task is a function of the number of processors alloted. The problem is motivated by real-life applications of parallel computer systems in scientific computing of highly parallelizable tasks. Starting from the continuous version of the problem (i. e. where the tasks may require a fractional part of the resources), we propose a general approximation algorithm with a performance guarantee equal to 2. Then, some improvements are derived that lead to a very good average behavior of the scheduling algorithm.Pozna

PARAMETER ANALYSIS OF CLUSTERS OF MELTING TEMPERATURES OF DNA CHAINS

In the paper the problem of DNA sequencing by hybridization (SBH) is considered.With the developed software, MELTEM, several assembling procedures are used to ease acollecting a subset of oligonucleotides that would melt under practically identical conditionsin a hybridization experiment. Some clustering approaches implemented in the program arecompared. The algorithms of MELTEM are presented as well as the selected examples of amelting temperature analysis.Pozna

Sequential algorithms for DNA sequencing

Reconstruction of the original DNA sequence in sequencing by hybridizationapproach (SBH) due to a large number of possible combinations requires acomputational support. In the paper, a new method of sequencing has beenproposed. Two algorithms based on its idea have been implemented and tested: forthe case of an ideal hybridization experiment (complete data) and for more generalcase, when some data are missing, like in the real experiment. Authentic DNAsequences have been used for testing. A parallel version of the second algorithm hasbeen also implemented and tested. The quality of the reconstruction is satisfactoryfor the library of oligunucleotides of length 9, and 100, 200 and 300-bp longsequences. A way to a further decrease of the computation time is also suggested,keywords: DNA sequencing,Pozna

A study of scheduling problems with preemptions on multi-core computers with GPU accelerators

International audienceFor many years, scheduling problems have been concerned either with parallel processor systems or with dedicated processors-job shop type systems. With a development of new computing architectures this partition is no longer so obvious. Multi-core (processor) computers equipped with GPU co-processors require new scheduling strategies. This paper is devoted to a characterization of this new type of scheduling problems. After a thorough introduction of the new model of a computing system, an extension of the classical notation of scheduling problems is proposed. A special attention is paid to preemptions, since this feature of the new architecture differs the most as compared with the classical model. In the paper, several scheduling algorithms, new ones and those refining classical approaches, are presented. Possible extensions of the model are also discussed

ProCKSI: a decision support system for Protein (Structure) Comparison, Knowledge, Similarity and Information

Background: We introduce the decision support system for Protein (Structure) Comparison, Knowledge, Similarity and Information (ProCKSI). ProCKSI integrates various protein similarity measures through an easy to use interface that allows the comparison of multiple proteins simultaneously. It employs the Universal Similarity Metric (USM), the Maximum Contact Map Overlap (MaxCMO) of protein structures and other external methods such as the DaliLite and the TM-align methods, the Combinatorial Extension (CE) of the optimal path, and the FAST Align and Search Tool (FAST). Additionally, ProCKSI allows the user to upload a user-defined similarity matrix supplementing the methods mentioned, and computes a similarity consensus in order to provide a rich, integrated, multicriteria view of large datasets of protein structures. Results: We present ProCKSI's architecture and workflow describing its intuitive user interface, and show its potential on three distinct test-cases. In the first case, ProCKSI is used to evaluate the results of a previous CASP competition, assessing the similarity of proposed models for given targets where the structures could have a large deviation from one another. To perform this type of comparison reliably, we introduce a new consensus method. The second study deals with the verification of a classification scheme for protein kinases, originally derived by sequence comparison by Hanks and Hunter, but here we use a consensus similarity measure based on structures. In the third experiment using the Rost and Sander dataset (RS126), we investigate how a combination of different sets of similarity measures influences the quality and performance of ProCKSI's new consensus measure. ProCKSI performs well with all three datasets, showing its potential for complex, simultaneous multi-method assessment of structural similarity in large protein datasets. Furthermore, combining different similarity measures is usually more robust than relying on one single, unique measure. Conclusion: Based on a diverse set of similarity measures, ProCKSI computes a consensus similarity profile for the entire protein set. All results can be clustered, visualised, analysed and easily compared with each other through a simple and intuitive interface

Sequential algorithms for DNA sequencing

Abstract Reconstruction of the original DNA sequence in sequencing by hybridization approach (SBH) due to a large number of possible combinations requires a computational support. In the paper, a new method of sequencing has been proposed. Two algorithms based on its idea have been implemented and tested: for the case of an ideal hybridization experiment (complete data) and for more general case, when some data are missing, like in the real experiment. Authentic DNA sequences have been used for testing. A parallel version of the second algorithm has been also implemented and tested. The quality of the reconstruction is satisfactory for the library of oligunucleotides of length 9, and 100, 200 and 300-bp long sequences. A way to a further decrease of the computation time is also suggested

Hepatitis C virus quasispecies in chronically infected children subjected to interferon–ribavirin therapy

Accumulating evidence suggests that certain features of hepatitis C virus (HCV), especially its high genetic variability, might be responsible for the low efficiency of anti-HCV treatment. Here, we present a bioinformatic analysis of HCV-1a populations isolated from 23 children with chronic hepatitis C (CHC) subjected to interferon–ribavirin therapy. The structures of the viral quasispecies were established based on a 132-amino-acid sequence derived from E1/E2 protein, including hypervariable region 1 (HVR1). Two types of HCV populations were identified. The first type, found in non-responders, contained a small number of closely related variants. The second type, characteristic for sustained responders, was composed of a large number of distantly associated equal-rank variants. Comparison of 445 HVR1 sequences showed that a significant number of variants present in non-responding patients are closely related, suggesting that certain, still unidentified properties of the pathogen may be key factors determining the result of CHC treatment