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28 articles for “Motif”
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Research ArticleOpen accessEvery word in the titleA Selection-based MCL Clustering Algorithm for Motif DiscoveryChunxiao Sun, Zhiyong Zhang, Jinglei Tang, Shuai LiuAs motif discovery plays an important role in the understanding of the relationship of gene regulation, this paper puts forward a selection-based MCL clustering refinement algorithm (SMCLR) aiming at solving the planted (l, d) motif search (PMS) problem. Firstly, we divide the DNA dataset into different subsets through selection of reference sequence and screen parts of eligible subsets by setting … …American Journal of Biochemistry and Biotechnology, Vol. 14, Issue 4 · 1 Jan 2019 · 8,827 accessesView PDFCite
Research ArticleOpen accessEvery word in the titleIn Silico Characterization and Motif Election of Neurotoxins from Snake VenomMahmudul Hasan, Ziaul Faruque Joy, Elius Hossain Bhuiyan, Md Shiful IslamSnake venom is a mixture of many biological components. Snakes usually use their venomic armory to tackle different prey and predators in adverse natural world. Among various components of the snake venom, neurotoxins play an important role in exerting effect by blocking the neuromuscular transmission through selective binding to muscle nicotinic Acetyl-Choline Receptors (nAChR). A set of 30 reference protein … …American Journal of Biochemistry and Biotechnology, Vol. 11, Issue 2 · 2 Mar 2015 · 7,702 accessesView PDFCite
Research ArticleOpen accessEvery word in the titleGenetic Algorithm Based Probabilistic Motif Discovery in Unaligned Biological SequencesM. Hemalatha, K. VivekanandanFinding motif in biosequences is the most important primitive operation in computational biology. There are many computational requirements for a motif discovery algorithm such as computer memory space requirement and computational complexity. To overcome the complexity of motif discovery, we propose an alternative solution integrating genetic algorithm and Fuzzy Art machine learning approaches for eliminating multiple sequence alignment process. Problem … …Journal of Computer Science, Vol. 4, Issue 8 · 31 Aug 2008 · 6,729 accessesView PDFCite
Research ArticleOpen accessEvery word in the titleIn silico and in vitro Structural Analysis on the Interaction of Calmodulin and Calmodulin-Binding Motif of FKBP35 from Plasmodium knowlesiSazlinawatie Aladin, Cahyo Budiman et al.FK506-binding protein 35 (FKBP35) is a peptidyl-prolyl cis-trans isomerase found in Plasmodium knowlesi, a zoonotic malaria parasite responsible for concerning cases of malaria infection in East Malaysia. This protein contains a segment known as the calmodulin-binding motif (Pk-CBM), which is predicted to facilitate interaction with calmodulin from P. knowlesi (Pk-CaM). Although this interaction is considered promising for future antimalarial drug … …OnLine Journal of Biological Sciences, Vol. 25, Issue 2 · 10 Mar 2025 · 4,846 accessesView PDFCite
Research ArticleOpen accessIn the keywordsCONTENT BASED BATIK IMAGE RETRIEVALA. Haris Rangkuti, Agus Harjoko, Agfianto Eko PutroContent Based Batik Image Retrieval (CBBIR) is an area of research that focuses on image processing based on characteristic motifs of batik. Basically the image has a unique batik motif compared with other images. Its uniqueness lies in the characteristics possessed texture and shape, which has a unique and distinct characteristics compared with other image characteristics. To study this batik … …Journal of Computer Science, Vol. 10, Issue 6 · 27 Jan 2014 · 7,417 accessesView PDFCite
Research ArticleOpen accessIn the keywordsDetecting Patterns in 5’ Untranslated Regions of Genes Involved in the Regulation of Blood Pressure and Oxidative StressMaria Sanchez-Aguilar, Luz Ibarra-Lara, Beatriz Zamora-Lopez et al.Hypertension is a chronic physical condition with multifactorial causes. Although genetic factors have been associated to this pathological condition, characterization of the sequence patterns in the regulatory sites, for example, in 3’ or 5’ Untranslated Regions (UTR), remains to be explored. In particular, the 5’ UTR of genes associated with the regulation of blood pressure and oxidative stress are analyzed … …Current Research in Medicine, Vol. 4, Issue 2 · 27 Nov 2013 · 7,283 accessesView PDFCite
Research ArticleOpen accessIn the keywordsBinding Studies of Natural Product Berberine with DNA G-QuadruplexNagendra K. Sharma, Pooja Lunawat, Manjusha DixitProblem statement: The ends of chromosome had highly repetitive short G and C-rich sequences of DNA. These sequences were known to form stable tetraplex type of secondary structures which help to maintain gene integratity after cell divison. Approach: Any reagent which controls the random cell division would be useful to design anticancer drugs. Therefore a many natural and synthesized molecules … …American Journal of Biochemistry and Biotechnology, Vol. 7, Issue 3 · 22 Sep 2011 · 8,797 accessesView PDFCite
Research ArticleOpen accessIn the keywordsFrequency of P/S(XX)P Duplication and FRFE, Absence of LYP in P6Gag of Indian Human Immunodeficiency Virus-1 Subtype C IsolatesKrutika Wadekar, Sudhanshu Pandey, Preeti Jain et al.Problem statement: The presence of a p6 domain at the C-terminus of the Gag polyprotein is a characteristic feature of HIV-1 and other primate lentiviruses. The p6Gag protein is considered as a major phosphoprotein in mature HIV-1 virions and is involved in the viral assembly and budding process. Sequence variation in the p6gag region in HIV-1 has been associated with … …Current Research in Medicine, Vol. 1, Issue 2 · 31 Oct 2010 · 7,529 accessesView PDFCite
Research ArticleOpen accessIn the keywordsApplication of RNA-DNA Duplex Base Triplets to Antisense DrugsJie Yang, Yao Leng, Ju BaoSixty-four sets of three-dimensional models of RNA-DNA duplex base triplets were constructed based on codons by homology modeling method using software InsightII on Indigo workstation, which should be helpful for the study of RNA-DNA annealing, the basis of nucleic acids interactions and some peculiar motifs for design antisense oligonucleotides. Our research result reveal that the energies (such as E, Ec, … …American Journal of Biochemistry and Biotechnology, Vol. 1, Issue 2 · 30 Jun 2005 · 6,531 accessesView PDFCite
Research ArticleOpen accessIn the keywordsDetermination of SVM-RBF Kernel Space Parameter to Optimize Accuracy Value of Indonesian Batik Images ClassificationAvinanta Tarigan, Dewi Agushinta, Adang Suhendra, Fikri BudimanImage retrieval using Support Vector Machine (SVM) classification verydepends on kernel function and parameter. Kernel function used by dot productsubstitution from old dimension feature to new dimension depends on imagedataset condition. In this research, parameter of Gaussian /Radial BasisFunction (RBF) kernel function is optimized using multi class non-linear SVMmethod and implemented to training and test datasets of traditional Indonesian batik … …Journal of Computer Science, Vol. 13, Issue 11 · 23 Oct 2017 · 7,530 accessesView PDFCite