Commenced in January 2007
Frequency: Monthly
Edition: International
Paper Count: 6

alignment Related Publications

6 CompPSA: A Component-Based Pairwise RNA Secondary Structure Alignment Algorithm

Authors: Ghada Badr, Arwa Alturki

Abstract:

The biological function of an RNA molecule depends on its structure. The objective of the alignment is finding the homology between two or more RNA secondary structures. Knowing the common functionalities between two RNA structures allows a better understanding and a discovery of other relationships between them. Besides, identifying non-coding RNAs -that is not translated into a protein- is a popular application in which RNA structural alignment is the first step A few methods for RNA structure-to-structure alignment have been developed. Most of these methods are partial structure-to-structure, sequence-to-structure, or structure-to-sequence alignment. Less attention is given in the literature to the use of efficient RNA structure representation and the structure-to-structure alignment methods are lacking. In this paper, we introduce an O(N2) Component-based Pairwise RNA Structure Alignment (CompPSA) algorithm, where structures are given as a component-based representation and where N is the maximum number of components in the two structures. The proposed algorithm compares the two RNA secondary structures based on their weighted component features rather than on their base-pair details. Extensive experiments are conducted illustrating the efficiency of the CompPSA algorithm when compared to other approaches and on different real and simulated datasets. The CompPSA algorithm shows an accurate similarity measure between components. The algorithm gives the flexibility for the user to align the two RNA structures based on their weighted features (position, full length, and/or stem length). Moreover, the algorithm proves scalability and efficiency in time and memory performance.

Keywords: Data Mining, alignment, RNA secondary structure, pairwise, component-based

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5 Alignment between Understanding and Assessment Practice among Secondary School Teachers

Authors: Eftah Bte. Moh @ Hj Abdullah, Izazol Binti Idris, Abd Aziz Bin Abd Shukor

Abstract:

This study aimed to identify the alignment of understanding and assessment practices among secondary school teachers. The study was carried out using quantitative descriptive study. The sample consisted of 164 teachers who taught Form 1 and 2 from 11 secondary schools in the district of North Kinta, Perak, Malaysia. Data were obtained from 164 respondents who answered Expectation Alignment Understanding and Practices of School Assessment (PEKDAPS) questionnaire. The data were analysed using SPSS 17.0+. The Cronbach’s alpha value obtained through PEKDAPS questionnaire pilot study was 0.86. The results showed that teachers' performance in PEKDAPS based on the mean value was less than 3, which means that perfect alignment does not occur between the understanding and practices of school assessment. Two major PEKDAPS sub-constructs of articulation across grade and age and usability of the system were higher than the moderate alignment of the understanding and practices of school assessment (Min=2.0). The content focused of PEKDAPs sub-constructs which showed lower than the moderate alignment of the understanding and practices of school assessment (Min=2.0). Another two PEKDAPS subconstructs of transparency and fairness and the pedagogical implications showed moderate alignment (2.0). The implications of the study is that teachers need to fully understand the importance of alignment among components of assessment, learning and teaching and learning objectives as strategies to achieve quality assessment process.

Keywords: understanding, alignment, assessment practices, School Based Assessment

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4 The Alignment of Information Systems and Environmental Organizations Model in Perspective Capability

Authors: Wartika, Kridanto Surendro, Husni Sastramiharja, Iping Supriana S.

Abstract:

The condition of the market is currently very dynamic, demanding organizations which is use system information to support the achievement of objectives should be necessarily improve the ability of information systems in accordance with the changes. Improved information systems capabilities need to align with the resource capabilities in internal environment of the organization, and vice versa. Alignment model between information systems and environment organizational in this capability perspective is expected can assist management in making the strategy for enhance the capability of information systems in accordance with resources internally within the organization, efficiency in the process of development, and optimization of contributions information systems in achieving organizational goals.

Keywords: Information System, alignment, capability, environmental organizations

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3 Alignment of Emission Gamma Ray Sources with Nai(Ti) Scintillation Detectors by Two Laser Beams to Pre-Operation using Alternating Minimization Technique

Authors: Abbas Ali Mahmood Karwi

Abstract:

Accurate timing alignment and stability is important to maximize the true counts and minimize the random counts in positron emission tomography So signals output from detectors must be centering with the two isotopes to pre-operation and fed signals into four units of pulse-processing units, each unit can accept up to eight inputs. The dual source computed tomography consist two units on the left for 15 detector signals of Cs-137 isotope and two units on the right are for 15 detectors signals of Co-60 isotope. The gamma spectrum consisting of either single or multiple photo peaks. This allows for the use of energy discrimination electronic hardware associated with the data acquisition system to acquire photon counts data with a specific energy, even if poor energy resolution detectors are used. This also helps to avoid counting of the Compton scatter counts especially if a single discrete gamma photo peak is emitted by the source as in the case of Cs-137. In this study the polyenergetic version of the alternating minimization algorithm is applied to the dual energy gamma computed tomography problem.

Keywords: Image, laser, detectors, spectrum, alignment

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2 Effect of Information System Strategies on Supply Chain Strategies and Supply Chain Performance

Authors: M. Khatami Rad, M. Torabizadeh, A. Noshadi

Abstract:

In order to achieve competitive advantage and better performance of firm, supply chain management (SCM) strategy should support and drive forward business strategy. It means that supply chain should be aligned with business strategy, at the same time supply chain (SC) managers need to use appropriate information system (IS) solution to support their strategy, which would lead to stay competitive. There are different kinds of IS strategies which enable managers to meet the SC requirement by selecting the best IS strategy. Therefore, it is important to align IS strategies and practices with SC strategies and practices, which could help us to plan for an IS application that supports and enhances a SCMS. In this study, aligning IS with SC in strategy level is considered. The main aim of this paper is to align the various IS strategies with SCM strategies and demonstrate their impact on SC and firm performance.

Keywords: supply chain strategy, alignment, Firm Performance, Information system strategy

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1 SAF: A Substitution and Alignment Free Similarity Measure for Protein Sequences

Authors: Abdellali Kelil, Shengrui Wang, Ryszard Brzezinski

Abstract:

The literature reports a large number of approaches for measuring the similarity between protein sequences. Most of these approaches estimate this similarity using alignment-based techniques that do not necessarily yield biologically plausible results, for two reasons. First, for the case of non-alignable (i.e., not yet definitively aligned and biologically approved) sequences such as multi-domain, circular permutation and tandem repeat protein sequences, alignment-based approaches do not succeed in producing biologically plausible results. This is due to the nature of the alignment, which is based on the matching of subsequences in equivalent positions, while non-alignable proteins often have similar and conserved domains in non-equivalent positions. Second, the alignment-based approaches lead to similarity measures that depend heavily on the parameters set by the user for the alignment (e.g., gap penalties and substitution matrices). For easily alignable protein sequences, it's possible to supply a suitable combination of input parameters that allows such an approach to yield biologically plausible results. However, for difficult-to-align protein sequences, supplying different combinations of input parameters yields different results. Such variable results create ambiguities and complicate the similarity measurement task. To overcome these drawbacks, this paper describes a novel and effective approach for measuring the similarity between protein sequences, called SAF for Substitution and Alignment Free. Without resorting either to the alignment of protein sequences or to substitution relations between amino acids, SAF is able to efficiently detect the significant subsequences that best represent the intrinsic properties of protein sequences, those underlying the chronological dependencies of structural features and biochemical activities of protein sequences. Moreover, by using a new efficient subsequence matching scheme, SAF more efficiently handles protein sequences that contain similar structural features with significant meaning in chronologically non-equivalent positions. To show the effectiveness of SAF, extensive experiments were performed on protein datasets from different databases, and the results were compared with those obtained by several mainstream algorithms.

Keywords: Protein, alignment, similarity, substitution

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