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Journal articles on the topic 'Motif comparison'

Author: Grafiati

Published: 20 February 2023

Last updated: 19 July 2025

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1

Xie, Chenwei, Qiao Ke, Haoyu Chen, Chuang Liu, and Xiu-Xiu Zhan. "Directed Network Comparison Using Motifs." Entropy 26, no. 2 (2024): 128. http://dx.doi.org/10.3390/e26020128.

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Analyzing and characterizing the differences between networks is a fundamental and challenging problem in network science. Most previous network comparison methods that rely on topological properties have been restricted to measuring differences between two undirected networks. However, many networks, such as biological networks, social networks, and transportation networks, exhibit inherent directionality and higher-order attributes that should not be ignored when comparing networks. Therefore, we propose a motif-based directed network comparison method that captures local, global, and higher

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CHEN, BRIAN Y., DREW H. BRYANT, VIACHESLAV Y. FOFANOV, et al. "CAVITY SCALING: AUTOMATED REFINEMENT OF CAVITY-AWARE MOTIFS IN PROTEIN FUNCTION PREDICTION." Journal of Bioinformatics and Computational Biology 05, no. 02a (2007): 353–82. http://dx.doi.org/10.1142/s021972000700276x.

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Algorithms for geometric and chemical comparison of protein substructure can be useful for many applications in protein function prediction. These motif matching algorithms identify matches of geometric and chemical similarity between well-studied functional sites, motifs, and substructures of functionally uncharacterized proteins, targets. For the purpose of function prediction, the accuracy of motif matching algorithms can be evaluated with the number of statistically significant matches to functionally related proteins, true positives (TPs), and the number of statistically insignificant mat

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Iyengar, Bharat Ravi, Beena Pillai, K. V. Venkatesh, and Chetan J. Gadgil. "Systematic comparison of the response properties of protein and RNA mediated gene regulatory motifs." Molecular BioSystems 13, no. 6 (2017): 1235–45. http://dx.doi.org/10.1039/c6mb00808a.

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Fotiadis, D. I., A. Likas, and K. Blekas. "A Sequential Method for Discovering Probabilistic Motifs in Proteins." Methods of Information in Medicine 43, no. 01 (2004): 9–12. http://dx.doi.org/10.1055/s-0038-1633414.

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Summary Objectives: This paper proposes a greedy algorithm for learning a mixture of motifs model through likelihood maximization, in order to discover common substrings, known as motifs, from a given collection of related biosequences. Methods: The approach sequentially adds a new motif component to a mixture model by performing a combined scheme of global and local search for appropriately initializing the component parameters. A hierarchical clustering scheme is also applied initially which leads to the identification of candidate motif models and speeds up the global searching procedure. R

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Schäfer, Patrick, and Ulf Leser. "Motiflets." Proceedings of the VLDB Endowment 16, no. 4 (2022): 725–37. http://dx.doi.org/10.14778/3574245.3574257.

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A time series motif intuitively is a short time series that repeats itself approximately the same within a larger time series. Such motifs often represent concealed structures, such as heart beats in an ECG recording, the riff in a pop song, or sleep spindles in EEG sleep data. Motif discovery (MD) is the task of finding such motifs in a given input series. As there are varying definitions of what exactly a motif is, a number of different algorithms exist. As central parameters they all take the length l of the motif and the maximal distance r between the motif's occurrences. In practice, howe

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Zhou, Lily, and Gabrielle L. Boulianne. "Comparison of the neuralized genes of Drosophila virilis and D. melanogaster." Genome 37, no. 5 (1994): 840–47. http://dx.doi.org/10.1139/g94-119.

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The neurogenic gene neuralized of Drosophila melanogaster is thought to play a role in the determination of cell fate in the embryonic nervous system as well as other tissues during development. To determine which sequences within the neuralized gene encode functionally important domains, we have initiated an interspecific comparison of the neuralized gene of D. virilis and D. melanogaster. In this study we show that several motifs that we have previously identified in the neuralized protein of D. melanogaster are conserved in D. virilis. These include a putative nuclear localization signal, a

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Meera, A., and Lalitha Rangarajan. "Comparison of Promoter Sequences Based on Inter Motif Distance." International Journal of Software Science and Computational Intelligence 3, no. 3 (2011): 57–68. http://dx.doi.org/10.4018/ijssci.2011070105.

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Understanding how the regulation of gene networks is orchestrated is an important challenge for characterizing complex biological processes. The DNA sequences that comprise promoters do not provide much direct information about regulation. A substantial part of the regulation results from the interaction of transcription factors (TFs) with specific cis regulatory DNA sequences. These regulatory sequences are organized in a modular fashion, with each module (enhancer) containing one or more binding sites for a specific combination of TFs. In the present work, the authors have proposed to invest

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Martins, Alexandra, Christian H. Gross, and Stewart Shuman. "Mutational Analysis of Vaccinia Virus Nucleoside Triphosphate Phosphohydrolase I, a DNA-Dependent ATPase of the DExH Box Family." Journal of Virology 73, no. 2 (1999): 1302–8. http://dx.doi.org/10.1128/jvi.73.2.1302-1308.1999.

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ABSTRACT Vaccinia virus nucleoside triphosphate phosphohydrolase I (NPH-I) is a DNA-dependent ATPase that serves as a transcription termination factor during viral mRNA synthesis. NPH-I is a member of the DExH box family of nucleic acid-dependent nucleoside triphosphatases (NTPases), which is defined by the presence of several conserved sequence motifs. We have assessed the contributions of individual amino acids (underlined) in motifs I (GxGKT), II (DExHN), III (SAT), and VI (QxxGRxxR) to ATP hydrolysis by performing alanine scanning mutagenesis. Significant decrements in ATPase activity resu

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Letzel, Tobias, Egbert Mundt, and Alexander E. Gorbalenya. "Evidence for functional significance of the permuted C motif in Co2+-stimulated RNA-dependent RNA polymerase of infectious bursal disease virus." Journal of General Virology 88, no. 10 (2007): 2824–33. http://dx.doi.org/10.1099/vir.0.82890-0.

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Segment B of bisegmented infectious bursal disease virus (IBDV) encodes virus protein 1 (VP1), possessing RNA-dependent RNA polymerase (RdRp) activity. This multidomain protein includes an RdRp domain with a non-canonical order of three sequence motifs forming the active site: C–A–B. The A–B–C order of the motifs, as found in RdRps of the majority of viruses, was converted by relocation (permutation) of motif C to a C–A–B order. Due to the unusual location and unproven significance, the motif was named ‘C?’. This motif includes an Ala–Asp–Asn tripeptide that replaces the C motif Gly–Asp–Asp se

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Zhang, Jian, Wei Wang, and Yingmei Li. "A characteristic comparison of cell-free DNA isolated from plasma and cerebrospinal fluid in patients with cancer." Journal of Clinical Oncology 41, no. 16_suppl (2023): e14008-e14008. http://dx.doi.org/10.1200/jco.2023.41.16_suppl.e14008.

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e14008 Background: Cell-free DNA (cfDNA) from plasma has proved its power as a liquid biopsy analyte in many cancer types, except cancers from central nervous system (CNS). CfDNA from cerebrospinal fluid (CSF) better recapitulates mutations for primary CNS tumors or cancer brain metastasis. The characteristics of cfDNA from plasma, including concentration range, mutation frequency, length, end motif etc. have been thoroughly studied, while the features of cfDNA from CSF are yet to be investigated. Methods: We retrospectively reviewed records since 2021 from a clinical sequencing center, and se

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CARAT, SOLENNE, RÉMI HOULGATTE, and JÉRÉMIE BOURDON. "A PARALLEL SCHEME FOR COMPARING TRANSCRIPTION FACTOR BINDING SITES MATRICES." Journal of Bioinformatics and Computational Biology 08, no. 03 (2010): 485–502. http://dx.doi.org/10.1142/s0219720010004689.

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Gene regulation implies many mechanisms. Their identification is a crucial task to construct regulatory networks, and is necessary to understand the pathology in many cases. This requires the identification of transcription factors that play a role in regulation. Numerous motif discovery tools are now available. Combining efficiently their results appears useful for comparing and clustering these motifs in order to reduce redundancies and to identify the corresponding transcription factor. We develop a method that produces, compares and clusters a set of motifs and identifies some close motifs

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Allam, Tahani M. "MOTIFSM: Cloudera Motif DNA Finding Algorithm." International Journal of Information Technology and Computer Science 15, no. 4 (2023): 10–18. http://dx.doi.org/10.5815/ijitcs.2023.04.02.

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Many studying systems of gene function work depend on the DNA motif. DNA motifs finding generate a lot of trails which make it complex. Regulation of gene expression is identified according to Transcription Factor Binding Sites (TFBSs). There are different algorithms explained, over the past decades, to get an accurate motif tool. The major problems for these algorithms are on the execution time and the memory size which depend on the probabilistic approaches. Our previous algorithm, called EIMF, is recently proposed to overcome these problems by rearranging data. Because cloud computing invol

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Low, Kok On. "Abu Nawas Sabah Folk Version: Intertextuality and Creativity." Malay Literature 28, no. 1 (2015): 1–31. http://dx.doi.org/10.37052/ml.28(1)no1.

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The tales of Abu Nawas, which originated in Arab-Persia are popular humorous stories told in the Malay world. Several written sources reveal that these tales spread to the Malay world between the 13th and 15th centuries, through the books One Thousand and One Nights and Hikayat Abu Nawas . Drawing from field trips conducted in a number of places in Sabah, a total of 13 tales, that had been transmitted orally among Sabah indigenous informants, have been collected. Upon comparison with Hikayat Abu Nawas , it was found that some of the Sabah folk version of Abu Nawas tales are similar to those pu

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Zhong, Xuehua, Neocles Leontis, Shuiming Qian, et al. "Tertiary Structural and Functional Analyses of a Viroid RNA Motif by Isostericity Matrix and Mutagenesis Reveal Its Essential Role in Replication." Journal of Virology 80, no. 17 (2006): 8566–81. http://dx.doi.org/10.1128/jvi.00837-06.

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ABSTRACT RNA-templated RNA replication is essential for viral or viroid infection, as well as for regulation of cellular gene expression. Specific RNA motifs likely regulate various aspects of this replication. Viroids of the Pospiviroidae family, as represented by the Potato spindle tuber viroid (PSTVd), replicate in the nucleus by utilizing DNA-dependent RNA polymerase II. We investigated the role of the loop E (sarcin/ricin) motif of the PSTVd genomic RNA in replication. A tertiary-structural model of this motif, inferred by comparative sequence analysis and comparison with nuclear magnetic

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WATTAM, Beth, Dazhuang SHANG, Salman RAHMAN та ін. "Arg-Tyr-Asp (RYD) and Arg-Cys-Asp (RCD) motifs in dendroaspin promote selective inhibition of β1 and β3 integrins". Biochemical Journal 356, № 1 (2001): 11–17. http://dx.doi.org/10.1042/bj3560011.

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Arg-Gly-Asp (RGD) is a unique minimal integrin-binding sequence that is found within several glycoprotein ligands. This sequence has also been found in snake-venom anti-platelet proteins, including the disintegrins and dendroaspin, a natural variant of short-chain neurotoxins isolated from the venom of Dendroaspis jamesonii. In the present study, the motifs RYD and RCD were introduced into the dendroaspin scaffold to replace RGD. Both motifs in dendroaspin caused inhibition of ADP-induced platelet aggregation with IC50 values of 200 and 300nM respectively, similar to that of the wild-type RGD

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Cserhati, Matyas. "Motif content comparison between monocot and dicot species." Genomics Data 3 (March 2015): 128–36. http://dx.doi.org/10.1016/j.gdata.2014.12.006.

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Mańka, Rafał, Pawel Janas, Karolina Sapoń, Teresa Janas, and Tadeusz Janas. "Role of RNA Motifs in RNA Interaction with Membrane Lipid Rafts: Implications for Therapeutic Applications of Exosomal RNAs." International Journal of Molecular Sciences 22, no. 17 (2021): 9416. http://dx.doi.org/10.3390/ijms22179416.

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RNA motifs may promote interactions with exosomes (EXO-motifs) and lipid rafts (RAFT-motifs) that are enriched in exosomal membranes. These interactions can promote selective RNA loading into exosomes. We quantified the affinity between RNA aptamers containing various EXO- and RAFT-motifs and membrane lipid rafts in a liposome model of exosomes by determining the dissociation constants. Analysis of the secondary structure of RNA molecules provided data about the possible location of EXO- and RAFT-motifs within the RNA structure. The affinity of RNAs containing RAFT-motifs (UUGU, UCCC, CUCC, CC

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Romanovа, L. N. "Plots and motifs of legends about Taas Ullungakh in folklore and literature: on the question of continued folklore traditions in the literature." Issues of National Literature, no. 4 (December 26, 2023): 72–82. http://dx.doi.org/10.25587/2782-6635-2023-4-72-82.

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The relevance of the research is due to the need to study the specifics of the interaction of folklore and literature from the point of view of the continuity of oral literature traditions and their artistic interpretation and transformation in Yakut literature. The problems of functioning and interpretation in the structure of the literary text of the folklore narrative are still poorly studied. Meanwhile, folk legends and legends are one of the important genre- and plot-forming components of Yakut literature. A comparison of plots and motifs of legends in folklore narratives and literary wor

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POLOULIAKH, NATALIA, TOHRU NATSUME, HAJIME HARADA, WATARU FUJIBUCHI, and PAUL HORTON. "COMPARATIVE GENOMIC ANALYSIS OF TRANSCRIPTION REGULATION ELEMENTS INVOLVED IN HUMAN MAP KINASE G-PROTEIN COUPLING PATHWAY." Journal of Bioinformatics and Computational Biology 04, no. 02 (2006): 469–82. http://dx.doi.org/10.1142/s0219720006001849.

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The identification of cis-elements (motifs) in the regulatory regions of higher eukaryotes is an important and challenging problem in computational biology. Eukaryotic transcriptional regulatory mechanisms pose several difficulties for promoter analysis: including a high variance in the motif locations, frequently large divergence from motif consensus patterns, and a large amount of repetitive elements (confusing to many motif finding procedures). One promising approach to this difficult problem involves cross-species comparison. In this work we analyzed the full-length regulatory regions of g

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Yousif, Ali Basim, Hussein Keitan Al-Khafaji, and Thekra Abbas. "A survey of exact motif finding algorithms." Indonesian Journal of Electrical Engineering and Computer Science 27, no. 2 (2022): 1109–18. https://doi.org/10.11591/ijeecs.v27.i2.pp1109-1118.

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Deoxyribonucleic acid (DNA) motif finding (discovery/mining) in biological chains is the most recent challenging and interesting trend in bioinformatics. It represents a crucial phase in most bioinformatics systems related to unravelling the secrets of gene functions. Despite the efforts made to date to produce robust algorithms, DNA motif finding remains a difficult task for researchers in this field. In general, biological pattern locating algorithms are categorized into two categories: probabilistic and numerical methods. In this paper, we provide a survey of exact DNA motif finding algorit

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Yanguas, Francisco, and M. Henar Valdivieso. "Analysis of the SNARE Stx8 recycling reveals that the retromer-sorting motif has undergone evolutionary divergence." PLOS Genetics 17, no. 3 (2021): e1009463. http://dx.doi.org/10.1371/journal.pgen.1009463.

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Fsv1/Stx8 is aSchizosaccharomyces pombeprotein similar to mammalian syntaxin 8.stx8Δcells are sensitive to salts, and the prevacuolar endosome (PVE) is altered instx8Δcells. These defects depend on the SNARE domain, data that confirm the conserved function of syntaxin8 and Stx8 in vesicle fusion at the PVE. Stx8 localizes at thetrans-Golgi network (TGN) and the prevacuolar endosome (PVE), and its recycling depends on the retromer component Vps35, and on the sorting nexins Vps5, Vps17, and Snx3. Several experimental approaches demonstrate that Stx8 is a cargo of the Snx3-retromer. Using extensi

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Groseth, Allison, Svenja Wolff, Thomas Strecker, Thomas Hoenen, and Stephan Becker. "Efficient Budding of the Tacaribe Virus Matrix Protein Z Requires the Nucleoprotein." Journal of Virology 84, no. 7 (2010): 3603–11. http://dx.doi.org/10.1128/jvi.02429-09.

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ABSTRACT The Z protein has been shown for several arenaviruses to serve as the viral matrix protein. As such, Z provides the principal force for the budding of virus particles and is capable of forming virus-like particles (VLPs) when expressed alone. For most arenaviruses, this activity has been shown to be linked to the presence of proline-rich late-domain motifs in the C terminus; however, for the New World arenavirus Tacaribe virus (TCRV), no such motif exists within Z. It was recently demonstrated that while TCRV Z is still capable of functioning as a matrix protein to induce the formatio

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Γαλανάκης, Αθανάσιος Β. "Yvan Goll – Ε. Χ. Γονατάς: Προς μια συγκριτική ποιητική". Σύγκριση 26 (25 лютого 2018): 11. http://dx.doi.org/10.12681/comparison.11120.

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This study aims to explore the relationship between the works of Yvan Goll and E. Ch. Gonatas. More specifically, the main purpose of the study is to highlight the role played by the Expressionist Movement (in which Yvan Goll was an active member) in the literary works of E. Ch. Gonatas. The methodological tools of Comparative Literature and Hermeneutics are used to prove the close relationship between the two authors and the expressionistic texture of their art. In the first part, the study is concerned with the expressionistic imagery, the poetics of landscape, the use of colors and the symb

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Martyanov, Viktor, and Robert H. Gross. "Transcriptional Regulation in the G1-S Cell Cycle Stage in Fungi: Insights through Computational Analysis." Open Bioinformatics Journal 6, no. 1 (2012): 43–54. http://dx.doi.org/10.2174/1875036201206010043.

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The transcription factor complexes Mlu1-box binding factor (MBF) and Swi4/6 cell cycle box binding factor (SBF) regulate the cell cycle in Saccharomyces cerevisiae. They activate hundreds of genes and are responsible for nor-mal cell cycle progression from G1 to S phase. We investigated the conservation of MBF and SBF binding sites during fungal evolution. Orthologs of S. cerevisiae targets of these transcription factors were identified in 37 fungal species and their upstream regions were analyzed for putative transcription factor binding sites. Both groups displayed enrichment in specific put

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Chen, Zhikui, Yin Peng, Shuo Yu, Chen Cao, and Feng Xia. "Subgraph Adaptive Structure-Aware Graph Contrastive Learning." Mathematics 10, no. 17 (2022): 3047. http://dx.doi.org/10.3390/math10173047.

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Graph contrastive learning (GCL) has been subject to more attention and been widely applied to numerous graph learning tasks such as node classification and link prediction. Although it has achieved great success and even performed better than supervised methods in some tasks, most of them depend on node-level comparison, while ignoring the rich semantic information contained in graph topology, especially for social networks. However, a higher-level comparison requires subgraph construction and encoding, which remain unsolved. To address this problem, we propose a subgraph adaptive structure-a

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Kızıl, Abuzer. "Labrys and Ears on the Orthostat Block in the Southern Cella Wall of Zeus Lepsynos Temple at Euromos: An Iconographic Approach." Belleten 89, no. 314 (2025): 1–25. https://doi.org/10.37879/belleten.2025.001.

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A depiction of a labrys is flanked with an ear motif on either side within tabula ansata on an external orthostat block on the southern cella wall of the Zeus Lepsynos Temple at Euromos in Caria. Although labrys, i.e., double-axe motif is encountered across a vast geography in Antiquity, it is known that this sacred symbol was identified with Zeus especially in Caria. Nevertheless, Zeus of Euromos holds a labrys in one hand and a scepter in the other. This article aims to attain a plausible conclusion through comparison with similar examples and iconographic interpretation of labrys symbol exe

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Leontis, Neocles B., and Eric Westhof. "The Annotation of RNA Motifs." Comparative and Functional Genomics 3, no. 6 (2002): 518–24. http://dx.doi.org/10.1002/cfg.213.

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The recent deluge of new RNA structures, including complete atomic-resolution views of both subunits of the ribosome, has on the one hand literally overwhelmed our individual abilities to comprehend the diversity of RNA structure, and on the other hand presented us with new opportunities for comprehensive use of RNA sequences for comparative genetic, evolutionary and phylogenetic studies. Two concepts are key to understanding RNA structure: hierarchical organization of global structure and isostericity of local interactions. Global structure changes extremely slowly, as it relies on conserved

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Maziarz, Marcin, Stefan Broselid, Vincent DiGiacomo та ін. "A biochemical and genetic discovery pipeline identifies PLCδ4b as a nonreceptor activator of heterotrimeric G-proteins". Journal of Biological Chemistry 293, № 44 (2018): 16964–83. http://dx.doi.org/10.1074/jbc.ra118.003580.

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Recent evidence has revealed that heterotrimeric G-proteins can be activated by cytoplasmic proteins that share an evolutionarily conserved sequence called the Gα-binding-and-activating (GBA) motif. This mechanism provides an alternative to canonical activation by G-protein–coupled receptors (GPCRs) and plays important roles in cell function, and its dysregulation is linked to diseases such as cancer. Here, we describe a discovery pipeline that uses biochemical and genetic approaches to validate GBA candidates identified by sequence similarity. First, putative GBA motifs discovered in bioinfor

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Schumacher, Maria A., and Wenjie Zeng. "Structures of the activator ofK. pneumoniabiofilm formation, MrkH, indicates PilZ domains involved in c-di-GMP and DNA binding." Proceedings of the National Academy of Sciences 113, no. 36 (2016): 10067–72. http://dx.doi.org/10.1073/pnas.1607503113.

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The pathogenesis ofKlebsiella pneumoniais linked to the bacteria’s ability to form biofilms. Mannose-resistantKlebsiella-like (Mrk) hemagglutinins are critical forK.pneumoniabiofilm development, and the expression of the genes encoding these proteins is activated by a 3′,5′-cyclic diguanylic acid (c-di-GMP)–regulated transcription factor, MrkH. To gain insight into MrkH function, we performed structural and biochemical analyses. Data revealed MrkH to be a monomer with a two-domain architecture consisting of a PilZ C-domain connected to an N domain that unexpectedly also harbors a PilZ-like fol

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Brody, Stuart. "A Comparison of the Neurospora and Drosophila Clocks." Journal of Biological Rhythms 35, no. 2 (2019): 119–33. http://dx.doi.org/10.1177/0748730419892434.

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In Neurospora and other fungi, the protein frequency (FRQ) is an integral part and a negative element in the fungal circadian oscillator. In Drosophila and many other higher organisms, the protein period (PER) is an integral part and a negative element of their circadian oscillator. Employing bioinformatic techniques, such as BLAST, CLUSTAL, and MEME (Multiple Em for Motif Elicitation), 11 regions (sequences) of potential similarity were found between the fungal FRQ and the Drosophila PER. Many of these FRQ regions are conserved in many fungal FRQ(s). Many of these PER regions are conserved in

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Arifin, Muhammad Zainul, and Arli A. Parikesit. "Bioinformatics tools to Predict N-myristoylation Site a Comparison Study." Indonesian Journal of Life Sciences | ISSN: 2656-0682 (online) 1, no. 1 (2019): 6–12. http://dx.doi.org/10.54250/ijls.v1i1.10.

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Protein N-myristoylation is the covalent attachment of myrstate, via an amide bond, to the N-terminal glycine residue of a nascent polypeptide assisted by myristol-CoA protein: N-myristoltransferases (NMT). PROSITE motif describes 5 amino acid after glycine site that would give rise to myristoylation site. However, applied to whole database extract, this motif give too many false postive results. Therefore 2 new tools were developed for N-myristoylation prediction.Taking physical properties into consideration inceases prediction scores greatly. However, these algorithms still cannot predict my

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Titisari, Manik Ayu, Yunia Dwie Nurcahyanie, Yanatra Budi Pramana, and Yitno Utomo. "THE USAGE OF EIGEN VALUE AND VECTOR TO DETERMINE THE PRIORITY OF FACTORS IN INDONESIAN BATIK PURCHASE." WAKTU: Jurnal Teknik UNIPA 20, no. 02 (2022): 83–87. http://dx.doi.org/10.36456/waktu.v20i02.5909.

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Modern batik is one of the fashion trends that are always in demand by the market. When choosing batik, many factors are considered including the type of batik (writing or stamp), fabric material, motif, quality, color, price, and design (model). Of all these factors, the most influencing people in buying batik are prices, motifs, colors, and designs (models). This study used Eigen Values and Vectors to determine the priority of factors that influence batik purchases. To find out the factors that are most in demand by the market among the four factors (price, motif, color, and design), the stu

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Cartwright, Eoin, Martin Crane, and Heather J. Ruskin. "Side-Length-Independent Motif (SLIM): Motif Discovery and Volatility Analysis in Time Series—SAX, MDL and the Matrix Profile." Forecasting 4, no. 1 (2022): 219–37. http://dx.doi.org/10.3390/forecast4010013.

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As the availability of big data-sets becomes more widespread so the importance of motif (or repeated pattern) identification and analysis increases. To date, the majority of motif identification algorithms that permit flexibility of sub-sequence length do so over a given range, with the restriction that both sides of an identified sub-sequence pair are of equal length. In this article, motivated by a better localised representation of variations in time series, a novel approach to the identification of motifs is discussed, which allows for some flexibility in side-length. The advantages of thi

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Kuntjoro-Jakti, R. A. Diah Resita I. "Ragam Hias Nusantara." Humaniora 1, no. 2 (2010): 246. http://dx.doi.org/10.21512/humaniora.v1i2.2866.

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Considering subsided natural resources, creative economic is a choice and proclaimed by Indonesian government on 2008. Design is one of creative economic components that has critical part in showing Indonesia’s identity in worldwide. So, Indonesian motifs as national culture richness played as a determined part in comparison between Indonesia and other nation’s masterpiece. This article is the first part from four parts. This part focuses more in describing basic visual art that becomes the strength of Indonesian motif design: dot and line, shape, texture, and colour.

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Laus, Gerhard, Volker Kahlenberg, Thomas Gelbrich, Sven Nerdinger, and Herwig Schottenberger. "Crystal structure of 3-bromo-2-hydroxybenzoic acid." Acta Crystallographica Section E Crystallographic Communications 71, no. 5 (2015): 531–35. http://dx.doi.org/10.1107/s2056989015007331.

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Mutual carboxyl–carboxyl O—H...O hydrogen bonds link the molecules of the title compound, C7H5BrO3, into centrosymmetric dimers which display a centralR22(8) ring motif. In addition, there is an intramolecular hydroxyl–carboxyl O—H...O interaction present. A comparison with the crystal structures of 59 other substituted derivatives of salicylic acid shows that both the centrosymmetric carboxyl–carboxyl O—H...O dimer and the stacking mode of molecules along the shortaaxis observed in the title structure are frequent packing motifs in this set.

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Gavrilenko, V. D. "The motif of returning home in the lyric poetry of Nikolay Rubtsov and Leonid Zavalnyuk." Vestnik of North-Eastern Federal University 20, no. 4 (2024): 64–75. http://dx.doi.org/10.25587/2222-5404-2023-20-4-64-75.

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The article is devoted to the study of the motif of returning to one’s homeland in the poetry of Nikolay Rubtsov and Leonid Zavalnyuk. The biographical research method makes it possible to identify the reasons that make the motif of returning to one’s homeland one of the key motifs in the poetry of Rubtsov and Zavalnyuk. The childhood of the poets, the early lost of mothers, the war years, both being orphans with living fathers, and being forced to leave their homes for many years. A comparative typological analysis allows us to identify the commonality in the revelation of this motif: the ret

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Vásquez, Andrea, and Camilo López. "In SilicoGenome Comparison and Distribution Analysis of Simple Sequences Repeats in Cassava." International Journal of Genomics 2014 (2014): 1–9. http://dx.doi.org/10.1155/2014/471461.

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We conducted a SSRs density analysis in different cassava genomic regions. The information obtained was useful to establish comparisons between cassava’s SSRs genomic distribution and those of poplar, flax, andJatropha. In general, cassava has a low SSR density (~50 SSRs/Mbp) and has a high proportion of pentanucleotides, (24,2 SSRs/Mbp). It was found that coding sequences have 15,5 SSRs/Mbp, introns have 82,3 SSRs/Mbp, 5′ UTRs have 196,1 SSRs/Mbp, and 3′ UTRs have 50,5 SSRs/Mbp. Through motif analysis of cassava’s genome SSRs, the most abundant motif was AT/AT while in intron sequences and UT

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BI, CHENGPENG. "SEAM: A STOCHASTIC EM-TYPE ALGORITHM FOR MOTIF-FINDING IN BIOPOLYMER SEQUENCES." Journal of Bioinformatics and Computational Biology 05, no. 01 (2007): 47–77. http://dx.doi.org/10.1142/s0219720007002527.

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Position weight matrix-based statistical modeling for the identification and characterization of motif sites in a set of unaligned biopolymer sequences is presented. This paper describes and implements a new algorithm, the Stochastic EM-type Algorithm for Motif-finding (SEAM), and redesigns and implements the EM-based motif-finding algorithm called deterministic EM (DEM) for comparison with SEAM, its stochastic counterpart. The gold standard example, cyclic adenosine monophosphate receptor protein (CRP) binding sequences, together with other biological sequences, is used to illustrate the perf

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Reuper, Hendrik, and Björn Krenz. "Comparison of two Turnip mosaic virus P1 proteins in their ability to co-localize with the Arabidopsis thaliana G3BP-2 protein." Virus Genes 57, no. 2 (2021): 233–37. http://dx.doi.org/10.1007/s11262-021-01829-w.

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AbstractTurnip mosaic virus (TuMV), belonging to the genus Potyvirus (family Potyviridae), has a large host range and consists of a single-stranded positive sense RNA genome encoding 12 proteins, including the P1 protease. This protein which is separated from the polyprotein by cis cleavage at its respective C-terminus, has been attributed with different functions during potyviral infection of plants. P1 of Turnip mosaic virus (P1-TuMV) harbors an FGSF-motif and FGSL-motif at its N-terminus. This motif is predicted to be a binding site for the host Ras GTPase-activating protein-binding protein

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Liu, Jing, Hussein A. Abbass, David G. Green, and Weicai Zhong. "Motif Difficulty (MD): A Predictive Measure of Problem Difficulty for Evolutionary Algorithms Using Network Motifs." Evolutionary Computation 20, no. 3 (2012): 321–47. http://dx.doi.org/10.1162/evco_a_00045.

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One of the major challenges in the field of evolutionary algorithms (EAs) is to characterise which kinds of problems are easy and which are not. Researchers have been attracted to predict the behaviour of EAs in different domains. We introduce fitness landscape networks (FLNs) that are formed using operators satisfying specific conditions and define a new predictive measure that we call motif difficulty (MD) for comparison-based EAs. Because it is impractical to exhaustively search the whole network, we propose a sampling technique for calculating an approximate MD measure. Extensive experimen

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Bich Thuy, Le Thi. "SIMILARITIES AND DIFFERENCES BETWEEN VIETNAMESE CULTURE AND LAO CULTURE THROUGH THE MOTIF OF BUILDING ORPHAN CHARACTERS IN THE MAGICAL FAIRY TALES OF TAM AND CAM AND THE GOLDEN TURTLE." Revista de Investigaciones Universidad del Quindío 32, no. 2 (2020): 102–14. http://dx.doi.org/10.33975/riuq.vol32n2.460.

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Sharing the sources of Southeast Asian folklore and folk literature, magical fairy tales of Vietnam and Laos have many similarities in a motif of building orphan characters. Applying structural theory in fairy tales with immutability and changes, the structure of the story is described by a series of events “signs help to make a schematic comparison of the structure of various tales,” (Propp, 1968, p.25) the article studies the magical fairy tale Tam and Cam of Vietnam and the Golden Turtle of Laos to see the similarities and differences in the motif of building orphan characters. The similari

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Alnasir, Jamie J., and Hugh P. Shanahan. "Transcriptomics: Quantifying Non-Uniform Read Distribution Using MapReduce." International Journal of Foundations of Computer Science 29, no. 08 (2018): 1355–72. http://dx.doi.org/10.1142/s0129054118430086.

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RNA-seq is a high-throughput Next-sequencing technique for estimating the concentration of all transcripts in a transcriptome. The method involves complex preparatory and post-processing steps which can introduce bias, and the technique produces a large amount of data [7, 19]. Two important challenges in processing RNA-seq data are therefore the ability to process a vast amount of data, and methods to quantify the bias in public RNA-seq datasets. We describe a novel analysis method, based on analysing sequence motif correlations, that employs MapReduce on Apache Spark to quantify bias in Next-

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Dhami, Jaya K., Kiersten M. Idzorek, Ryan B. Johnson, Kaitlyn S. Van Auken, and William H. Ojala. "Intramolecular geometry and intermolecular interactions of the CNO group of crystalline benzonitrile oxides: a comparison with phenyl cyanates, phenyl isocyanates, and phenyl azides." CrystEngComm 21, no. 5 (2019): 908–16. http://dx.doi.org/10.1039/c8ce02008f.

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Custódio, Tânia Filipa, Peter Aasted Paulsen, Kelly May Frain, and Bjørn Panyella Pedersen. "Structural comparison of GLUT1 to GLUT3 reveal transport regulation mechanism in sugar porter family." Life Science Alliance 4, no. 4 (2021): e202000858. http://dx.doi.org/10.26508/lsa.202000858.

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The human glucose transporters GLUT1 and GLUT3 have a central role in glucose uptake as canonical members of the Sugar Porter (SP) family. GLUT1 and GLUT3 share a fully conserved substrate-binding site with identical substrate coordination, but differ significantly in transport affinity in line with their physiological function. Here, we present a 2.4 Å crystal structure of GLUT1 in an inward open conformation and compare it with GLUT3 using both structural and functional data. Our work shows that interactions between a cytosolic “SP motif” and a conserved “A motif” stabilize the outward confo

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Rostovtseva, Yu A. "A sailing ship as a motif and symbol in The Life [Zhitie] of Archpriest Avvakum." Voprosy literatury, no. 5 (October 30, 2022): 84–98. http://dx.doi.org/10.31425/0042-8795-2022-5-84-98.

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The article is concerned with the motif and symbol of a sailing ship in The Life [Zhitie] of Archpriest Avvakum. The researcher is the first to challenge the supposition about a ‘traditional’ genesis of this motif and symbol in Avvakum’s autobiography; she also defines the role of this motif in the plot of The Life — the magnum opus of the Old Believers’ spiritual leader. Various motif-related elements are ancillary to the main idea of The Life — to demonstrate the hero’s sainthood. The same message guides Avvakum’s choice of sources to borrow the main motif and symbol for his book. Among thes

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Jonassen, Christine M., Tom Ø. Jonassen, Yehia M. Saif, et al. "Comparison of capsid sequences from human and animal astroviruses." Journal of General Virology 82, no. 5 (2001): 1061–67. http://dx.doi.org/10.1099/0022-1317-82-5-1061.

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We have sequenced the genomic 3′-end, including the structural gene, of human astrovirus (HAstV) serotype 7 and morphologically related viruses infecting pig (PAstV), sheep (OAstV) and turkey (TAstV-1). These sequences were compared with corresponding astrovirus sequences available in the nucleic acid databases, including sequences of the seven other HAstV serotypes, two other avian astroviruses (TAstV-2 and avian nephritis virus) and astrovirus from cat (FAstV). A 35 nt stem–loop motif near the 3′-end of the genome, previously described as being highly conserved, was present in all of the ast

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McGuire, Gabriel Vertin. "Trickster, Comrade, Citizen: The Adventures of Aldar Köse in Kazakh Folktales and Mass Culture." Journal of American Folklore 135, no. 537 (2022): 281–304. http://dx.doi.org/10.5406/15351882.135.537.02.

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Abstract This paper traces the path of Motif K111.1, Alleged gold-dropping animal sold, through a series of tales in which the trickster Aldar Köse works his way to wealth through ruses that exploit the norms and institutions of mobile pastoral production. Comparison of the motif across eras reveals the ways in which a trickster figure who embodied a disorderly anarchy of appetite was improbably reborn as an apostle of order.

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PROSPERI, MATTIA C. F., LUCIANO PROSPERI, REBECCA R. GRAY, and MARCO SALEMI. "ON COUNTING THE FREQUENCY DISTRIBUTION OF STRING MOTIFS IN MOLECULAR SEQUENCES." International Journal of Biomathematics 05, no. 06 (2012): 1250055. http://dx.doi.org/10.1142/s1793524512500556.

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This work investigates frequency distributions of strings within a text. The mathematical derivation accounts for variable alphabet size, character probabilities, and string/text lengths, under both the Bernoullian and the Markovian model for string generation. The analysis is limited to the set of non-clumpable strings, that cannot overlap with themselves. Two formulae (exact and approximated) are derived, calculating the frequency distribution of a string of length m found inside a text of length n (with m < n). The approximated formula has a constant complexity (in contrast to an exponen

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Rodriguez Buitrago, Jhon Alexander, Thomas Klünemann, Wulf Blankenfeldt, and Anett Schallmey. "Expression, purification and crystal structure determination of a ferredoxin reductase from the actinobacterium Thermobifida fusca." Acta Crystallographica Section F Structural Biology Communications 76, no. 8 (2020): 334–40. http://dx.doi.org/10.1107/s2053230x2000922x.

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The ferredoxin reductase FdR9 from Thermobifida fusca, a member of the oxygenase-coupled NADH-dependent ferredoxin reductase (FNR) family, catalyses electron transfer from NADH to its physiological electron acceptor ferredoxin. It forms part of a putative three-component cytochrome P450 monooxygenase system in T. fusca comprising CYP222A1 and the [3Fe–4S]-cluster ferredoxin Fdx8 as well as FdR9. Here, FdR9 was overexpressed and purified and its crystal structure was determined at 1.9 Å resolution. The overall structure of FdR9 is similar to those of other members of the FNR family and is compo

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Yousif, Ali Basim, Hussein Keitan Al-Khafaji, and Thekra Abbas. "A survey of exact motif finding algorithms." Indonesian Journal of Electrical Engineering and Computer Science 27, no. 2 (2022): 1109. http://dx.doi.org/10.11591/ijeecs.v27.i2.pp1109-1118.

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<span lang="EN-US"><span lang="EN-US">Deoxyribonucleic </span>acid (DNA) motif finding (discovery/mining) in biological chains is the most recent challenging and interesting trend in bioinformatics. It represents a crucial phase in most bioinformatics systems related to unravelling the secrets of gene functions. Despite the efforts made to date to produce robust algorithms, DNA motif finding remains a difficult task for researchers in this field. In general, biological pattern locating algorithms are categorized into two categories: probabilistic and numerical methods. In thi

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