A multiple alignment program for protein sequences

A program for the multiple alignment of protein sequences is presented. The program is an extension of the fast alignment program by Wilbur et al. (1984) into higher dimensions. The use of hash procedures on fragments of the protein sequences increases the speed of calculation. Thereby we also take into account fragments which are present in some, but not in all, sequences considered. The results of some multiple alignments are given.     

一种多处理器平台上的传感器事务调度算法

如何有效地调度传感器事务以维护数据的时态一致性是信息物理融合系统研究中的一个重要问题。已有的调度算法基本上都是针对单处理器平台来设计的。提出一种多处理器平台上的传感器事务调度算法,算法通过合理地分配和调整事务实例执行所需处理器资源来保证数据的时态一致性约束,通过预先计算出全局重复调度序列来降低运行开销,给出了算法的可调度性分析。实验结果表明,该算法具有较高的调度成功率,其产生的更新负载也较低。     

一种基于蚁群算法的生物序列并行比对方法

生物序列比对是生物信息领域的重要课题,比对结果的合理性和正确性关系到基于比对结果研究的正确性。在保证正确性的前提下利用并行计算充分挖掘计算潜力对提高比对效率有重要意义。针对双序列的全局比对问题,提出了基于蚁群算法的双序列比对并行化方案。对耗时最多的搜索比对路径和信息素更新两个步骤给出了基于共享内存模型的并行化方法。"天河二号"上OpenMP实验结果表明,8线程并行情况下,加速比可达5.03,且序列越长性能越高。     

MASH: an interactive program for multiple alignment and consensus sequence construction for biological sequences

This paper presents a method for the multiple alignment of a sequence set. The MASH algorithm uses a non-redundant database of common motifs and an 'alignment priority' criterion that depends on the length and the occurrence frequency of the patterns in the set of sequences. This user-defined criterion allows the determination of the series of the patterns to be aligned. This program is applied to a fragment of envelope gene env gp120 for 20 isolates of the immunodeficiency virus. The multiplicity of alignments obtained by modifying the criterion parameters reveals different aspects of similarity between the sequences.     

M-CASH: A real-time resource reclaiming algorithm for multiprocessor platforms

Resource reclaiming schemes are typically applied in reservation-based real-time uniprocessor systems to support efficient reclaiming and sharing of computational resources left unused by early completing tasks, improving the response times of aperiodic and soft tasks in the presence of overruns. In this paper, we introduce a novel and efficient reclaiming algorithm, named M-CASH, for multiprocessor platforms. M-CASH leverages the resource reservation approach offered by the Multiprocessor CBS server offering significant improvements. The correctness of the algorithm is formally proven and its performance is evaluated through extensive synthetic simulations.

A parallel strategy for biological sequence alignment in restricted memory space

Recently, many organisms had their DNA entirely sequenced, and this reality presents the need for aligning long DNA sequences, which is a challenging task due to its high demands for computational power and memory. The algorithm proposed by Smith–Waterman (SW) is an exact method that obtains optimal local alignments in quadratic space and time. For long sequences, quadratic complexity makes the use of this algorithm impractical. In this scenario, parallel computing is a very attractive alternative. In this paper, we propose and evaluate z-align, a parallel exact strategy based on the divergence concept to locally align long biological sequences using an affine gap function. Z-align runs in limited memory space, where the amount of memory used can be defined by the user. The results collected in a cluster with 16 processors presented very good speedups for long real DNA sequences. With z-align, we were able to compare up to 3 MBP (mega base-pairs) DNA sequences. As far as we know, this is the first time 3 MBP sequences are compared with an affine gap exact variation of the SW algorithm. Also, by comparing the results obtained with z-align and the popular BLAST tool, it is clear that z-align is able to produce longer and more significant alignments.     

On the design of high-performance algorithms for aligning multiple protein sequences on mesh-based multiprocessor architectures

In this paper, we address the problem of multiple sequence alignment (MSA) for handling very large number of proteins sequences on mesh-based multiprocessor architectures. As the problem has been conclusively shown to be computationally complex, we employ divisible load paradigm (also, referred to as divisible load theory, DLT) to handle such large number of sequences. We design an efficient computational engine that is capable of conducting MSAs by exploiting the underlying parallelism embedded in the computational steps of multiple sequence algorithms. Specifically, we consider the standard Smith–Waterman (SW) algorithm in our implementation, however, our approach is by no means restrictive to SW class of algorithms alone. The treatment used in this paper is generic to a class of similar dynamic programming problems. Our approach is recursive in the sense that the quality of solutions can be refined continuously till an acceptable level of quality is achieved. After first phase of computation, we design a heuristic scheme that renders the final solution for MSA. We conduct rigorous simulation experiments using several hundreds of homologous protein sequences derived from the Rattus Norvegicus and Mus Musculus databases of olfactory receptors. We quantify the performance based on speed-up metric. We compare our algorithms to serial or single machine processing approaches. We testify our findings by comparing with conventional equal load partitioning (ELP) strategy that is commonly used in the parallel processing literature. Based on our extensive simulation study, we observe that DLT paradigm offers an excellent speed-up characteristics and provides avenues for its use in several other biological sequence processing related problem. This study is a first time attempt in using the DLT paradigm to devise efficient strategies to handle large scale multiple protein sequence alignment problem on mesh-based multiprocessor systems.     

多处理器EPDFPfair算法的可调度性判定

针对多处理器实时调度中的最早伪时限优先(EPDF)Pfair算法,分析了EPDF算法在M个处理器平台上的可调度利用率约束,根据基于利用率的充分可调度性判定,提出了一种改进的可调度性判定方法。这种方法可以得到更多的可调度任务集,从而使得满足判定的强实时系统和使用tie-breaking规则困难的动态任务系统的调度有较小的开销。实验结果表明,改进的可调度性判定方法增加了判为可调度的任务集数量,具有较好的性能。     

A novel randomized iterative strategy for aligning multiple protein sequences.

The rigorous alignment of multiple protein sequences becomes impractical even with a modest number of sequences, since computer memory and time requirements increase as the product of the lengths of the sequences. We have devised a strategy to approach such an optimal alignment, which modifies the intensive computer storage and time requirements of dynamic programming. Our algorithm randomly divides a group of unaligned sequences into two subgroups, between which an optimal alignment is then obtained by a Needleman-Wunsch style of algorithm. Our algorithm uses a matrix with dimensions corresponding to the lengths of the two aligned sequence subgroups. The pairwise alignment process is repeated using different random divisions of the whole group into two subgroups. Compared with the rigorous approach of solving the n-dimensional lattice by dynamic programming, our iterative algorithm results in alignments that match or are close to the optimal solution, on a limited set of test problems. We have implemented this algorithm in a computer program that runs on the IBM PC class of machines, together with a user-friendly environment for interactively selecting sequences or groups of sequences to be aligned either simultaneously or progressively.     

Laxity dynamics and LLF schedulability analysis on multiprocessor platforms

LLF (Least Laxity First) scheduling, which assigns a higher priority to a task with a smaller laxity, has been known as an optimal preemptive scheduling algorithm on a single processor platform. However, little work has been made to illuminate its characteristics upon multiprocessor platforms. In this paper, we identify the dynamics of laxity from the system??s viewpoint and translate the dynamics into LLF multiprocessor schedulability analysis. More specifically, we first characterize laxity properties under LLF scheduling, focusing on laxity dynamics associated with a deadline miss. These laxity dynamics describe a lower bound, which leads to the deadline miss, on the number of tasks of certain laxity values at certain time instants. This lower bound is significant because it represents invariants for highly dynamic system parameters (laxity values). Since the laxity of a task is dependent of the amount of interference of higher-priority tasks, we can then derive a set of conditions to check whether a given task system can go into the laxity dynamics towards a deadline miss. This way, to the author??s best knowledge, we propose the first LLF multiprocessor schedulability test based on its own laxity properties. We also develop an improved schedulability test that exploits slack values. We mathematically prove that the proposed LLF tests dominate the state-of-the-art EDZL tests. We also present simulation results to evaluate schedulability performance of both the original and improved LLF tests in a quantitative manner.     

Algorithms for implementing elastic tasks on multiprocessor platforms: a comparative evaluation

Real-Time Systems - The elastic task model enables the adaptation of systems of recurrent real-time tasks under uncertain or potentially overloaded conditions. A range of permissible periods is...     

多处理器全局单调比率的可调度性分析

针对全局单调比率(RM)调度的多处理器系统中最高优先级任务数量少于处理器数量时,Bertogna等给出的最坏情况计算任务受到的干涉过于悲观,证明了任务受到最高优先级任务的干涉不会出现最坏情况,它受到非最高优先级任务干涉仍可能出现最坏情况。分析得出了任务受到最高优先级任务干涉的最大可能值,由此得到了一个更紧的可调度性判断条件。实验结果表明,提出的方法提高了判为可调度的任务集数量。     

Improving multiple sequence alignment biological accuracy through genetic algorithms

Accuracy on multiple sequence alignments (MSA) is of great significance for such important biological applications as evolution and phylogenetic analysis, homology and domain structure prediction. In such analyses, alignment accuracy is crucial. In this paper, we investigate a combined scoring function capable of obtaining a good approximation to the biological quality of the alignment. The algorithm uses the information obtained by the different quality scores in order to improve the accuracy. The results show that the combined score is able to evaluate alignments better than the isolated scores.     

A genetic algorithm for multiple sequence alignment

Multiple sequence alignment is an important tool in molecular sequence analysis. This paper presents genetic algorithms to solve multiple sequence alignments. Several data sets are tested and the experimental results are compared with other methods. We find our approach could obtain good performance in the data sets with high similarity and long sequences.The software can be found in http://rsdb.csie.ncu.edu.tw/tools/msa.htm.     

The feasibility of general task systems with precedence constraints on multiprocessor platforms

Feasibility analysis determines (prior to system execution-time) whether a specified collection of hard-real-time jobs executed on a processing platform can meet all deadlines. In this paper, we derive near-optimal sufficient tests for determining whether a given collection of jobs can feasibly meet all deadlines upon a specified multiprocessor platform assuming job migration is permitted. The collection of jobs may contain precedence constraints upon the order of execution of these jobs. The derived tests are general enough to be applied even when the collection of jobs is incompletely specified. We discuss the applicability of these tests to the scheduling of collections of jobs that are generated by systems of recurrent real-time tasks. We also show that our feasibility conditions may be used to obtain global-EDF schedulability conditions.

Simulating asynchronous hardware on multiprocessor platforms: the case of AMULET1

Synchronous VLSI design is approaching a critical point, with clock distribution becoming an increasingly costly and complicated issue and power consumption rapidly emerging as a major concern. Hence, recently, there has been a resurgence of interest in asynchronous digital design techniques which promise to liberate digital design from the inherent problems of synchronous systems. This activity has revealed a need for modelling and simulation techniques suitable for the asynchronous design style. The concurrent process algebra communicating sequential processes (CSP) and its executable counterpart, occam, are increasingly advocated as particularly suitable for this purpose. This paper focuses on issues related to the execution of CSP/occam models of asynchronous hardware on multiprocessor machines, including I/O, monitoring and debugging, partition, mapping and load balancing. These issues are addressed in the context of occarm, an occam simulation model of the AMULET1 asynchronous microprocessor; however, the solutions devised are more general and may be applied to other systems too. Copyright © 2001 John Wiley & Sons, Ltd.     

SOMAP: a novel interactive approach to multiple protein sequences alignment

A novel interactive method for generating multiple protein sequence alignments is described. The program has no internal limit to the number or length of sequences it can handle and is designed for use with DEC VAX processors running the VMS operating system. The approach used is essentially one of manual sequence manipulation, aided by built-in symbolic displays of identities and similarities, and strict and 'fuzzy' (ambiguous) pattern-matching facilities. Additional flexibility is provided by means of an interface to a publicly available automatic alignment system and to a comprehensive sequence analysis package.