A Comparative Analysis of Motif Discovery Algorithms
Issue:
Volume 4, Issue 1, February 2016
Pages:
1-9
Received:
25 September 2015
Accepted:
26 October 2015
Published:
19 November 2015
Abstract: One of the major challenges in bioinformatics is the development of efficient computational algorithms for biological sequence motif discovery. In the post-genomic era, the ability to predict the behavior, the function, or the structure of biological entities or motifs such as genes and proteins, as well as interactions among them, play a fundamental role in the discovery of information to help explain biological mechanisms. This necessitated the development of computational methods for identifying these entities. Consequently, a large number of motif finding algorithms have been implemented and applied to various organisms over the past decade. This paper presents a comparative analysis of the latest developments in motif finding algorithms and proposed an algorithm for motif discovery based on a combinatorial approach of pattern driven and statistical based approach. The proposed algorithm, Suffix Tree Gene Enrichment Motif Searching (STGEMS) as reported in [30], proved effective in identifying motifs from organisms with peculiarity in their genomic structure such as the AT-rich sequence of the malaria parasite, P. falciparum. The empirical time analysis of seven motif discovery algorithms was evaluated using four sets of genes from the intraerythrocytic development cycle of P. falciparum. The result shows that algorithms based on a combinatorial approach are more desirable.
Abstract: One of the major challenges in bioinformatics is the development of efficient computational algorithms for biological sequence motif discovery. In the post-genomic era, the ability to predict the behavior, the function, or the structure of biological entities or motifs such as genes and proteins, as well as interactions among them, play a fundament...
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The Role of Calcium on the Active Site of Snake Venom Phospholipase A2: Molecular Dynamics Simulations
Akubugwo Emmanuel I.,
Okafor Irene N.,
Ezebuo Fortunatus C.,
Lukong Colin B.,
Ifemeje Jonathan C.,
Nwaka Andrew C.,
Chilaka Ferdinand C.
Issue:
Volume 4, Issue 1, February 2016
Pages:
10-14
Received:
18 January 2016
Accepted:
28 January 2016
Published:
17 February 2016
Abstract: Snake venoms are rich in phospholipase A2 (PLA2) and their hydrolysis of cell membrane phospholipids explains the role of the enzyme in venom toxicity. Calcium is known to plays important role at the active site of PLA2 during catalysis. In this study, molecular dynamics simulations of free PLA2 and calcium bound PLA2 were carried out using GROMACS 4.5.5 to evaluate the role of calcium in PLA2 catalysis. The results showed that calcium induced formation of helical structures between Arg62 - Lys66, Asn107 - Tyr111 and Asp114 - Cys119 in PLA2 which with time disappeared through the formation and opening of loops. Calcium induced atomistic movements and conformational changes in snake venom PLA2 which led to the formation of a widened cleft at the active site of calcium bound PLA2 when compared with free PLA2. This could lead to a better binding and accommodation of substrate, thus enhancing catalysis. This study confirms the role of calcium towards the action of PLA2 in snake venom toxicity and could provide useful information for the design of small molecules that can function as PLA2 inhibitors.
Abstract: Snake venoms are rich in phospholipase A2 (PLA2) and their hydrolysis of cell membrane phospholipids explains the role of the enzyme in venom toxicity. Calcium is known to plays important role at the active site of PLA2 during catalysis. In this study, molecular dynamics simulations of free PLA2 and calcium bound PLA2 were carried out using GROMACS...
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