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Article
Publication date: 25 June 2020

Abedalmuhdi Almomany, Ahmad M. Al-Omari, Amin Jarrah and Mohammad Tawalbeh

The problem of motif discovery has become a significant challenge in the era of big data where there are hundreds of genomes requiring annotations. The importance of…

Abstract

Purpose

The problem of motif discovery has become a significant challenge in the era of big data where there are hundreds of genomes requiring annotations. The importance of motifs has led many researchers to develop different tools and algorithms for finding them. The purpose of this paper is to propose a new algorithm to increase the speed and accuracy of the motif discovering process, which is the main drawback of motif discovery algorithms.

Design/methodology/approach

All motifs are sorted in a tree-based indexing structure where each motif is created from a combination of nucleotides: ‘A’, ‘C’, ‘T’ and ‘G’. The full motif can be discovered by extending the search around 4-mer nucleotides in both directions, left and right. Resultant motifs would be identical or degenerated with various lengths.

Findings

The developed implementation discovers conserved string motifs in DNA without having prior information about the motifs. Even for a large data set that contains millions of nucleotides and thousands of very long sequences, the entire process is completed in a few seconds.

Originality/value

Experimental results demonstrate the efficiency of the proposed implementation; as for a real-sequence of 1,270,000 nucleotides spread into 2,000 samples, it takes 5.9 s to complete the overall discovering process when the code ran on an Intel Core i7-6700 @ 3.4 GHz machine and 26.7 s when running on an Intel Xeon x5670 @ 2.93 GHz machine. In addition, the authors have improved computational performance by parallelizing the implementation to run on multi-core machines using the OpenMP framework. The speedup achieved by parallelizing the implementation is scalable and proportional to the number of processors with a high efficiency that is close to 100%.

Details

Engineering Computations, vol. 38 no. 1
Type: Research Article
ISSN: 0264-4401

Keywords

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Article
Publication date: 25 September 2019

Afaf Abu Sirhan, Khalid Mohamad Abdrabbo, Serhan Ahmed Ali Al Tawalbeh, Mustafa Hamdi Ahmed and Mohammad Ali Helalat

The purpose of this paper is to illustrate some methods to protect digital libraries using digital rights management (DRM) technologies and specifically the methods…

Abstract

Purpose

The purpose of this paper is to illustrate some methods to protect digital libraries using digital rights management (DRM) technologies and specifically the methods applied at the digital libraries of Jordan universities.

Design/methodology/approach

A descriptive research method has been used to examine the extent of DRM in digital libraries of universities in Jordan.

Findings

Majority of the universities in Jordan use different methods of protection including coding, identification, authenticity and digital watermark. However, methods including digital signature, digital fingerprint, copy detection systems and pay system have not been employed within Jordanian universities. The use of copyright management systems has been limited, which shows the weakness in the use of technological protection within the investigated libraries.

Originality/value

This study has shown contribution to the development of digital libraries that are based on the protection of new technology and are able to provide better services to users without concern about protecting publishers’ rights.

Details

Library Management, vol. 40 no. 8/9
Type: Research Article
ISSN: 0143-5124

Keywords

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