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Milan Randic - One of the best experts on this subject based on the ideXlab platform.
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unique Graphical Representation of protein sequences based on nucleotide triplet codons
Chemical Physics Letters, 2004Co-Authors: Milan Randic, Jure Zupan, Alexandru T BalabanAbstract:We consider a Graphical Representation of proteins as an alternative to the usual Representation of proteins as a sequence listing the natural amino acids. The approach is based on a Graphical Representation of triplets of DNA in which the interior of a square or the interior of a tetrahedron is used to accommodate 64 sites for the 64 codons. By associating a zigzag curve and various matrices with a protein, just as was the case with Graphical Representation of DNA, one can construct selected invariants to serve as protein descriptors. The approach is illustrated on the A-chain of human insulin.
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compact 2 d Graphical Representation of dna
Chemical Physics Letters, 2003Co-Authors: Milan Randic, Jure Zupan, Marjan Vracko, Marjana NovicAbstract:Abstract We present a novel 2-D Graphical Representation for DNA sequences which has an important advantage over the existing Graphical Representations of DNA in being very compact. It is based on: (1) use of binary labels for the four nucleic acid bases, and (2) use of the ‘worm’ curve as template on which binary codes are placed. The approach is illustrated on DNA sequences of the first exon of human β-globin and gorilla β-globin.
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analysis of similarity dissimilarity of dna sequences based on novel 2 d Graphical Representation
Chemical Physics Letters, 2003Co-Authors: Milan Randic, Marjan Vracko, Nella Lers, Dejan PlavsicAbstract:The recently proposed 2-D Graphical Representation of DNA based on four horizontal lines involves an arbitrary assignment of the four types of bases to the lines. While each such assignment is legitimate, it is desirable to have a scheme free of such arbitrary choices among non-equivalent geometrical Representations. We outline one such approach, which is based on the construction of a 12-component vector whose components are the leading eigenvalues of the L/L matrices associated with DNA. The examination of similarities/dissimilarities among the coding sequences of the first exon of b-globin gene of different species illustrates the utility of the approach. 2003 Elsevier Science B.V. All rights reserved.
Bo Liao - One of the best experts on this subject based on the ideXlab platform.
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a 2d Graphical Representation of dna sequence based on dual nucleotides and its application
International Journal of Quantum Chemistry, 2009Co-Authors: Zanbo Liu, Bo Liao, Wen Zhu, Guohua HuangAbstract:From the perspective of the neighboring dual nucleotides, we introduce a novel 2D Graphical Representation of DNA sequences based on the magic circle, which correspond to 16 dual nucleotides. So, we can reduce a DNA sequence into a plot set in two-dimensional space and get a two-component vector relatively to the introduced covariance matrix. The utility of our approach can be illustrated by the examination of similarities/dissimilarities among the complete coding sequences of β-globin gene belonging to 11 species. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
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on 2d Graphical Representation of dna sequence of nondegeneracy
Chemical Physics Letters, 2005Co-Authors: Yusen Zhang, Bo Liao, Kequan DingAbstract:Abstract Some two-dimensional (2D) Graphical Representations of DNA sequences have been given by Gates, Nandy, Leong and Mogenthaler, Randic, and Liao et al., which give visual characterizations of DNA sequences. In this Letter, we introduce a nondegeneracy 2D Graphical Representation of DNA sequence, which is different from Randic’s novel 2D Representation and Liao’s 2D Representation. We also present the nondegeneracy forms corresponding to the Representations of Gates, Nandy, Leong and Mogenthaler.
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analysis of similarity dissimilarity of dna sequences based on 3 d Graphical Representation
Chemical Physics Letters, 2004Co-Authors: Bo Liao, Tianming WangAbstract:Recently, we proposed a 3-D Graphical Representation of DNA sequences [Chem. Phys. Lett. 379 (2003) 412]. Based on this Representation, we outline one such approach by constructing a 15-component vector whose components are the average bandwidth of the D/D matrices. The examination of similarities/dissimilarities among the coding sequences of the first exon of β-globin gene of different species illustrates the utility of the approach.
Jie Wen - One of the best experts on this subject based on the ideXlab platform.
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new 3d Graphical Representation of dna sequence based on dual nucleotides
Journal of Theoretical Biology, 2007Co-Authors: Jie WenAbstract:We introduce a 3D Graphical Representation of DNA sequences based on the pairs of dual nucleotides (DNs). Based on this Representation, we consider some mathematical invariants and construct two 16-component vectors associated with these invariants. The vectors are used to characterize and compare the complete coding sequence part of beta globin gene of nine different species. The examination of similarities/dissimilarities illustrates the utility of the approach.
Sáez Riquelme Beatriz - One of the best experts on this subject based on the ideXlab platform.
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Bricked vaults of the 18th century Valencian hall churches: Graphical Representation, constructive and pathological analysis
'Universitat Politecnica de Valencia', 2018Co-Authors: Sáez Riquelme BeatrizAbstract:[EN] The efficient recovery of historic buildings is only possible through a deep knowledge of traditional construction systems. This article focuses on the study and analysis of the vaults of a group of temples located in the Spanish Levante region, the Valencian hall churches, inspired by the European architectural model known as “Hallenkirche”. Erected during the second half of the 18th century, to the north of the Valencian Community, they make up a constructive group limited in space and time, likely to constitute an ideal entity for investigation. The peculiarity of this type of churches lies in its vaults, which spring from a common height. The main contribution of this research is its Graphically schematized constructive classification, as well as the unveiling of their composition and the verification of the use of various counterfort systems. This study concludes with the analysis of the aforementioned vaults pathologies, derived from possible structural movements and expressed in the form of fissures, providing the classification thereof based on their location, and quantifying and assessing them. In order to achieve the stated objectives, it has been necessary to carry out technical inspections of the vaults, both from their intrados and extrados, obtaining data through its direct intake and through deduction methods.Thank you to all the bishoprics, parish priests and individual who facilitated our research by providing us access to the temples subject of this study.Saez Riquelme, B. (2018). Bricked vaults of the 18th century Valencian hall churches: Graphical Representation, constructive and pathological analysis. VITRUVIO - International Journal of Architectural Technology and Sustainability. 3(1):72-87. doi:10.4995/vitruvio-ijats.2018.10091SWORD72873
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Bricked vaults of the 18th century Valencian hall churches: Graphical Representation, constructive and pathological analysis
'Universitat Politecnica de Valencia', 2018Co-Authors: Sáez Riquelme BeatrizAbstract:[EN] The efficient recovery of historic buildings is only possible through a deep knowledge of traditional construction systems. This article focuses on the study and analysis of the vaults of a group of temples located in the Spanish Levante region, the Valencian hall churches, inspired by the European architectural model known as “Hallenkirche”. Erected during the second half of the 18th century, to the north of the Valencian Community, they make up a constructive group limited in space and time, likely to constitute an ideal entity for investigation. The peculiarity of this type of churches lies in its vaults, which spring from a common height. The main contribution of this research is its Graphically schematized constructive classification, as well as the unveiling of their composition and the verification of the use of various counterfort systems. This study concludes with the analysis of the aforementioned vaults pathologies, derived from possible structural movements and expressed in the form of fissures, providing the classification thereof based on their location, and quantifying and assessing them. In order to achieve the stated objectives, it has been necessary to carry out technical inspections of the vaults, both from their intrados and extrados, obtaining data through its direct intake and through deduction methods.Thank you to all the bishoprics, parish priests and individual who facilitated our research by providing us access to the temples subject of this study.Saez Riquelme, B. (2018). Bricked vaults of the 18th century Valencian hall churches: Graphical Representation, constructive and pathological analysis. VITRUVIO - International Journal of Architectural Technology and Sustainability. 3(1):72-87. doi:10.4995/vitruvio-ijats.2018.10091SWORD728731Bautista i García, J. D. (2002). Esglésies-saló del segle XVIII a les comarques valencianes. Fundación Dávalos-Fletcher, Castellón.Bérchez Gómez, J. (1987). Los comienzos de la arquitectura académica en Valencia: Antonio Gilabert. Federico Doménech, S.A. Valencia.Bérchez Gómez, J. y Corell Farinos, V. (1981). Catálogo de Diseños de Arquitectura de la Real Academia de BB.AA. de San Carlos de Valencia. 1768-1846. Colegio Oficial de Arquitectos de Valencia y Murcia, Valencia.Choisy, A. (1883). L'art de batir chez les byzantins, in Calvo López, J. (2012) Cantería y albañilería en los tratados de arquitectura y la práctica constructiva, Seminario Albañilería frente a cantería. Materiales, técnica y mecánica estructural. 23-24 marzo 2012, Universidad Politécnica de Valencia, Valencia.Gil Saura, Y. (2004). Arquitectura Barroca en Castellón. Diputación de Castellón, Castellón.Fornés y Gurrea, M. (1841). Observaciones sobre la práctica del arte de edificar. Imprenta Cabrerizo, Valencia.Fray Lorenzo de San Nicolás (1663). Arte y uso de Architectura. 2ª Parte.Huerta Fernández, S. (2004). Arcos, bóvedas y cúpulas. Geometría y equilibrio en el cálculo tradicional de estructuras de fábrica. Tesis. Instituto Juan de Herrera, Madrid.Huerta Fernández, S. (1999). La mecánica de las Bóvedas tabicadas en su contexto histórico: la aportación de los Guastavino, in Huerta Las bóvedas de Guastavino en América, Instituto Juan Herrera, Madrid.Más Torrecillas, V. J. (2008). Arquitectura social y estado entre 1939 y 1957. La dirección general de regiones devastadas. Tesis doctoral, UNED.Martínez Frías, J.M. (1980). El gótico en Soria. Arquitectura y escultura monumental, Salamanca. Diputación provincial, Salamanca.Pitarch Roig, A y Sáez Riquelme, B. (2009). La cúpula de Villahermosa del Río, en el inicio de la construcción academicista. In Huerta et al. Actas del Sexto Congreso Nacional de Historia de la construcción, Vol. II, Instituto Juan de Herrera, Madrid.Ricci, M. (2004). La cúpula, las máquinas y otros en la Florencia de Brunelleschi. Universidad Politécnica de Valencia, Valencia.Sáez Riquelme, B. (2013). Iglesias salón valencianas del XVIII: levantamiento gráfico, análisis geométrico y constructivo, patología común (Tesis). Universitat Jaume I, Castellón.Sáez Riquelme, B. (2017). Formal features of 18th century valencian hall churches. EGA. Revista de expresión gráfica arquitectónica (29). https://doi.org/10.4995/ega.2017.1463Sáez Riquelme, B. y Pitarch Roig, A.M. (2012). Algunas lesiones comunes de las iglesias salón: San Pedro en Cinctorres, San Jaime en Vila-real, San Martín en Callosa de Segura. In 4º Congreso internacional de patología y rehabilitación de edificios. PATORREBSáez Riquelme, B. y Pitarch Roig, A.M. (2015). Combination of technologies for architectural planning. Parish church of Portell. Revista de Expresión Gráfica Arquitectónica, 9. ISSN: 1888-8143Soler Verdú, R. y Soler Estrela, A. (2012). Navegando por el trasdós de las bóvedas tabicadas: tipos constructivos y noticia de artefactos construidos. In Construyendo bóvedas tabicadas, Actas del Simposio sobre Bóvedas tabicadas. Universidad Politécnica de Valencia, Valencia.Thomson Llisterri, T. (2006). Iglesia de Santa María la Mayor de Alcañiz. Centro de Estudios Bajoaragoneses, Alcañiz.Thunnissen, H. (2012). Bóvedas: su construcción y empleo en la construcción. Instituto Juan Herrera, Madrid.Vegas Lopez, F. & Mileto, C. (2012). Guastavino y el eslabón perdido, in Construyendo bóvedas tabicadas, Simposio sobre Bóvedas tabicadas. Universidad Politécnica de Valencia, Valencia.Vila Estébez, D.; Soler Estrela, A; Sáez Riquelme B. (2016). Los planos originales de la Iglesia Arciprestal de Vila-Real. Interpretación constructiva de la cúpula dibujada. In Dibujar, Construir, Soñar. Tirant Lo Blanc, Valencia
Jialiang Yang - One of the best experts on this subject based on the ideXlab platform.
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a dynamic 3d Graphical Representation for rna structure analysis and its application in non coding rna classification
PLOS ONE, 2016Co-Authors: Yi Zhang, Haiyun Huang, Xiaoqing Dong, Yiliang Fang, Kejing Wang, Lijuan Zhu, Ke Wang, Tao Huang, Jialiang YangAbstract:With the development of new technologies in transcriptome and epigenetics, RNAs have been identified to play more and more important roles in life processes. Consequently, various methods have been proposed to assess the biological functions of RNAs and thus classify them functionally, among which comparative study of RNA structures is perhaps the most important one. To measure the structural similarity of RNAs and classify them, we propose a novel three dimensional (3D) Graphical Representation of RNA secondary structure, in which an RNA secondary structure is first transformed into a characteristic sequence based on chemical property of nucleic acids; a dynamic 3D graph is then constructed for the characteristic sequence; and lastly a numerical characterization of the 3D graph is used to represent the RNA secondary structure. We tested our algorithm on three datasets: (1) Dataset I consisting of nine RNA secondary structures of viruses, (2) Dataset II consisting of complex RNA secondary structures including pseudo-knots, and (3) Dataset III consisting of 18 non-coding RNA families. We also compare our method with other nine existing methods using Dataset II and III. The results demonstrate that our method is better than other methods in similarity measurement and classification of RNA secondary structures.