Relevant bibliographies by topics / Sequence motif

Contents

  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers
  6. Reports

Academic literature on the topic 'Sequence motif'

Author: Grafiati
Published: 4 June 2021
Last updated: 20 February 2023

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Journal articles on the topic "Sequence motif"

1

Roebuck, K. A., D. P. Szeto, K. P. Green, Q. N. Fan, and W. E. Stumph. "Octamer and SPH motifs in the U1 enhancer cooperate to activate U1 RNA gene expression." Molecular and Cellular Biology 10, no. 1 (January 1990): 341–52. http://dx.doi.org/10.1128/mcb.10.1.341-352.1990.

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The transcriptional enhancer of a chicken U1 small nuclear RNA gene has been shown to extend over approximately 50 base pairs of DNA sequence located 180 to 230 base pairs upstream of the U1 transcription initiation site. It is composed of multiple functional motifs, including a GC box, an octamer motif, and a novel SPH motif. The contributions of these three distinct sequence motifs to enhancer function were studied with an oocyte expression assay. Under noncompetitive conditions in oocytes, the SPH motif is capable of stimulating U1 RNA transcription in the absence of the other functional mo
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Roebuck, K. A., D. P. Szeto, K. P. Green, Q. N. Fan, and W. E. Stumph. "Octamer and SPH motifs in the U1 enhancer cooperate to activate U1 RNA gene expression." Molecular and Cellular Biology 10, no. 1 (January 1990): 341–52. http://dx.doi.org/10.1128/mcb.10.1.341.

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The transcriptional enhancer of a chicken U1 small nuclear RNA gene has been shown to extend over approximately 50 base pairs of DNA sequence located 180 to 230 base pairs upstream of the U1 transcription initiation site. It is composed of multiple functional motifs, including a GC box, an octamer motif, and a novel SPH motif. The contributions of these three distinct sequence motifs to enhancer function were studied with an oocyte expression assay. Under noncompetitive conditions in oocytes, the SPH motif is capable of stimulating U1 RNA transcription in the absence of the other functional mo
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XING, ERIC P., WEI WU, MICHAEL I. JORDAN, and RICHARD M. KARP. "LOGOS: A MODULAR BAYESIAN MODEL FOR DE NOVO MOTIF DETECTION." Journal of Bioinformatics and Computational Biology 02, no. 01 (March 2004): 127–54. http://dx.doi.org/10.1142/s0219720004000508.

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The complexity of the global organization and internal structure of motifs in higher eukaryotic organisms raises significant challenges for motif detection techniques. To achieve successful de novo motif detection, it is necessary to model the complex dependencies within and among motifs and to incorporate biological prior knowledge. In this paper, we present LOGOS, an integrated LOcal and GlObal motif Sequence model for biopolymer sequences, which provides a principled framework for developing, modularizing, extending and computing expressive motif models for complex biopolymer sequence analy
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Zhai, Xiandun, and Adilai Tuerxun. "DNA Sequence Specificity Prediction Algorithm Based on Artificial Intelligence." Mathematical Problems in Engineering 2022 (October 3, 2022): 1–8. http://dx.doi.org/10.1155/2022/4150106.

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DNA sequence specificity refers to the ability of DNA sequences to bind specific proteins. These proteins play a central role in gene regulation such as transcription and alternative splicing. Obtaining DNA sequence specificity is very important for establishing the regulatory model of the biological system and identifying pathogenic variants. Motifs are sequence patterns shared by fragments of DNA sequences that bind to specific proteins. At present, some motif mining algorithms have been proposed, which perform well under the condition of given motif length. This research is based on deep le
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Wang, Mengchi, David Wang, Kai Zhang, Vu Ngo, Shicai Fan, and Wei Wang. "Motto: Representing Motifs in Consensus Sequences with Minimum Information Loss." Genetics 216, no. 2 (August 19, 2020): 353–58. http://dx.doi.org/10.1534/genetics.120.303597.

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Sequence analysis frequently requires intuitive understanding and convenient representation of motifs. Typically, motifs are represented as position weight matrices (PWMs) and visualized using sequence logos. However, in many scenarios, in order to interpret the motif information or search for motif matches, it is compact and sufficient to represent motifs by wildcard-style consensus sequences (such as [GC][AT]GATAAG[GAC]). Based on mutual information theory and Jensen-Shannon divergence, we propose a mathematical framework to minimize the information loss in converting PWMs to consensus seque
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Wright, Elisé P., Mahmoud A. S. Abdelhamid, Michelle O. Ehiabor, Melanie C. Grigg, Kelly Irving, Nicole M. Smith, and Zoë A. E. Waller. "Epigenetic modification of cytosines fine tunes the stability of i-motif DNA." Nucleic Acids Research 48, no. 1 (November 28, 2019): 55–62. http://dx.doi.org/10.1093/nar/gkz1082.

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Abstract i-Motifs are widely used in nanotechnology, play a part in gene regulation and have been detected in human nuclei. As these structures are composed of cytosine, they are potential sites for epigenetic modification. In addition to 5-methyl- and 5-hydroxymethylcytosine modifications, recent evidence has suggested biological roles for 5-formylcytosine and 5-carboxylcytosine. Herein the human telomeric i-motif sequence was used to examine how these four epigenetic modifications alter the thermal and pH stability of i-motifs. Changes in melting temperature and transitional pH depended on b
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MAURER-STROH, SEBASTIAN, HE GAO, HAO HAN, LIES BAETEN, JOOST SCHYMKOWITZ, FREDERIC ROUSSEAU, LOUXIN ZHANG, and FRANK EISENHABER. "MOTIF DISCOVERY WITH DATA MINING IN 3D PROTEIN STRUCTURE DATABASES: DISCOVERY, VALIDATION AND PREDICTION OF THE U-SHAPE ZINC BINDING ("HUF-ZINC") MOTIF." Journal of Bioinformatics and Computational Biology 11, no. 01 (February 2013): 1340008. http://dx.doi.org/10.1142/s0219720013400088.

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Data mining in protein databases, derivatives from more fundamental protein 3D structure and sequence databases, has considerable unearthed potential for the discovery of sequence motif—structural motif—function relationships as the finding of the U-shape (Huf-Zinc) motif, originally a small student's project, exemplifies. The metal ion zinc is critically involved in universal biological processes, ranging from protein-DNA complexes and transcription regulation to enzymatic catalysis and metabolic pathways. Proteins have evolved a series of motifs to specifically recognize and bind zinc ions.
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Liu, Xiang-Qin, and Jing Yang. "Bacterial Thymidylate Synthase with Intein, Group II Intron, and Distinctive ThyX Motifs." Journal of Bacteriology 186, no. 18 (September 15, 2004): 6316–19. http://dx.doi.org/10.1128/jb.186.18.6316-6319.2004.

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ABSTRACT The ThyX class of thymidylate synthases was previously characterized by a common ThyX motif, RHRX7S. We report bacterial ThyX sequences having distinctive ThyX motifs, suggesting a more general ThyX motif, R/THRX7-8S. One ThyX sequence has an intein in its ThyX motif that was shown to do protein splicing and a group II intron in its gene, suggesting a hot spot for these self-splicing mobile elements.
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Pal, Soumitra, Jan Hoinka, and Teresa M. Przytycka. "Co-SELECT reveals sequence non-specific contribution of DNA shape to transcription factor binding in vitro." Nucleic Acids Research 47, no. 13 (June 21, 2019): 6632–41. http://dx.doi.org/10.1093/nar/gkz540.

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Abstract Understanding the principles of DNA binding by transcription factors (TFs) is of primary importance for studying gene regulation. Recently, several lines of evidence suggested that both DNA sequence and shape contribute to TF binding. However, the following compelling question is yet to be considered: in the absence of any sequence similarity to the binding motif, can DNA shape still increase binding probability? To address this challenge, we developed Co-SELECT, a computational approach to analyze the results of in vitro HT-SELEX experiments for TF–DNA binding. Specifically, Co-SELEC
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Gunawardana, D., V. A. Likic, and K. R. Gayler. "A Comprehensive Bioinformatics Analysis of the Nudix Superfamily inArabidopsis thaliana." Comparative and Functional Genomics 2009 (2009): 1–13. http://dx.doi.org/10.1155/2009/820381.

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Nudix enzymes are a superfamily with a conserved common reaction mechanism that provides the capacity for the hydrolysis of a broad spectrum of metabolites. We used hidden Markov models based on Nudix sequences from the PFAM and PROSITE databases to identify Nudix hydrolases encoded by theArabidopsisgenome. 25 Nudix hydrolases were identified and classified into 11 individual families by pairwise sequence alignments. Intron phases were strikingly conserved in each family. Phylogenetic analysis showed that all multimember families formed monophyletic clusters. Conserved familial sequence motifs
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Dissertations / Theses on the topic "Sequence motif"

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Leung, Chi-ming. "Motif discovery for DNA sequences." Click to view the E-thesis via HKUTO, 2006. http://sunzi.lib.hku.hk/hkuto/record/B3859755X.

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Leung, Chi-ming, and 梁志銘. "Motif discovery for DNA sequences." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2006. http://hub.hku.hk/bib/B3859755X.

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Liu, Agatha H. "Motif-based mining of protein sequences /." Thesis, Connect to this title online; UW restricted, 2002. http://hdl.handle.net/1773/6894.

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Dinh, Hieu Trung. "Algorithms for DNA Sequence Assembly and Motif Search." University of Connecticut, 2013.

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Siu, Man-hung. "Finding motif pairs from protein interaction networks." Click to view the E-thesis via HKUTO, 2008. http://sunzi.lib.hku.hk/hkuto/record/B40987760.

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Siu, Man-hung, and 蕭文鴻. "Finding motif pairs from protein interaction networks." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2008. http://hub.hku.hk/bib/B40987760.

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Al-Ouran, Rami. "Motif Selection: Identification of Gene Regulatory Elements using Sequence CoverageBased Models and Evolutionary Algorithms." Ohio University / OhioLINK, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=ohiou1449003717.

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Lin, Jasper Chua. "Application of the Trp-cage motif to polypeptide folding questions /." Thesis, Connect to this title online; UW restricted, 2007. http://hdl.handle.net/1773/8684.

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Chen, Bernard. "Discovery and Extraction of Protein Sequence Motif Information that Transcends Protein Family Boundaries." Digital Archive @ GSU, 2009. http://digitalarchive.gsu.edu/cs_diss/42.

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Protein sequence motifs are gathering more and more attention in the field of sequence analysis. The recurring patterns have the potential to determine the conformation, function and activities of the proteins. In our work, we obtained protein sequence motifs which are universally conserved across protein family boundaries. Therefore, unlike most popular motif discovering algorithms, our input dataset is extremely large. As a result, an efficient technique is essential. We use two granular computing models, Fuzzy Improved K-means (FIK) and Fuzzy Greedy K-means (FGK), in order to efficient
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Pei, Shermin. "Identification of functional RNA structures in sequence data." Thesis, Boston College, 2016. http://hdl.handle.net/2345/bc-ir:107275.

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Thesis advisor: Michelle M. Meyer<br>Thesis advisor: Peter Clote<br>Structured RNAs have many biological functions ranging from catalysis of chemical reactions to gene regulation. Many of these homologous structured RNAs display most of their conservation at the secondary or tertiary structure level. As a result, strategies for natural structured RNA discovery rely heavily on identification of sequences sharing a common stable secondary structure. However, correctly identifying the functional elements of the structure continues to be challenging. In addition to studying natural RNAs, we improv
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Books on the topic "Sequence motif"

1

A motif of mathematics: [history and application of the mediant and the Farey sequence]. Boston: Docent Press, 2011.

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Aitken, Alastair. Identification of protein consensus sequences: Active site motifs, phosphorylation, and other post-translational modifications. New York: Ellis Horwood, 1990.

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Aitken, Alastair. Identification of protein consensus sequences: Active site motifs, phosphorylation, and other post-translational modifications. New York: Ellis Horwood, 1990.

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Comics and the city: Urban space in print, picture, and sequence. New York: Continuum, 2010.

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Taylor, Catherine Yvonne. Analysis of protein binding motifs in the nucleotide sequence of the human [gamma]-actin gene promoter. Ottawa: National Library of Canada = Bibliothèque nationale du Canada, 1993.

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Sun, Qing. Generation and characterization of antibodies with defined specificity towards fibronectin-binding sequences within the D-motifs of staphylococcus. Ottawa: National Library of Canada, 1998.

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Rowett, Catherine. Introduction and Summary for Part IV: Plato’s Theaetetus. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780199693658.003.0009.

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The chapter summarizes the results of Part IV and explains and introduces the work on the Theaetetus in Chapters 10, 11, and 12. It explains what misguided assumptions undermine all Theaetetus’s attempts to define knowledge (focusing especially on the reductionist assumptions throughout the dialogue). Second, it examines the significance of the motif of the midwife, whose task is twofold: first to provide life-saving aids for each failing infant, and then to judge its viability once those aids are in place. The dialogue therefore manifests an alternating sequence of constructive work, to prop
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Identification of Protein Consensus Sequences: Active Site Motifs, Phosphorylation, and Other Posttranslational Modifications (Ellis Horwood Books in the Biological Sciences). Ellis Horwood Ltd, 1990.

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Hicks, Matthew Raymond. Coiled-coil assembly by proteins and peptides with unusual sequence motifs. 2000.

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(Contributor), P. Bengert, T. Dandekar (Contributor), D. Ostareck (Contributor), A. Ostareck-Lederer (Contributor), and Thomas Dandekar (Editor), eds. RNA Motifs and Regulatory Elements. 2nd ed. Springer, 2002.

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Book chapters on the topic "Sequence motif"

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Han, Shin-Kap. "Motif of Sequence, Motif in Sequence." In Life Course Research and Social Policies, 21–38. Cham: Springer International Publishing, 2014. http://dx.doi.org/10.1007/978-3-319-04969-4_2.

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Kim, Ju Han. "Motif and Regulatory Sequence Analysis." In Genome Data Analysis, 189–211. Singapore: Springer Singapore, 2019. http://dx.doi.org/10.1007/978-981-13-1942-6_11.

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Chen, Bernard. "Protein Sequence Motif Information Discovery." In Algorithmic and Artificial Intelligence Methods for Protein Bioinformatics, 41–55. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2013. http://dx.doi.org/10.1002/9781118567869.ch2.

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Liang, Jie, and Ronald Jackups. "Sequence and Spatial Motif Discovery in Short Sequence Fragments." In Encyclopedia of Algorithms, 1945–52. New York, NY: Springer New York, 2016. http://dx.doi.org/10.1007/978-1-4939-2864-4_601.

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Liang, Jie, and Ronald Jackups. "Sequence and Spatial Motif Discovery in Short Sequence Fragments." In Encyclopedia of Algorithms, 1–10. Boston, MA: Springer US, 2014. http://dx.doi.org/10.1007/978-3-642-27848-8_601-1.

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Liu, Jin S., Mayetri Gupta, Xiaole Liu, Linda Mayerhofere, and Charles E. Lawrence. "Statistical Models for Biological Sequence Motif Discovery." In Case Studies in Bayesian Statistics, 3–32. New York, NY: Springer New York, 2002. http://dx.doi.org/10.1007/978-1-4612-2078-7_1.

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Wyatt, Jacqueline R., and C. A. Stein. "Oligonucleotides Containing the G-Quartet Sequence Motif." In Applications of Antisense Therapies to Restenosis, 133–40. Boston, MA: Springer US, 1999. http://dx.doi.org/10.1007/978-1-4615-5183-6_8.

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Zheleva, Elena, and Abdullah N. Arslan. "Fast Motif Search in Protein Sequence Databases." In Computer Science – Theory and Applications, 670–81. Berlin, Heidelberg: Springer Berlin Heidelberg, 2006. http://dx.doi.org/10.1007/11753728_67.

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Ceci, Michelangelo, Corrado Loglisci, Eliana Salvemini, Domenica D’Elia, and Donato Malerba. "Mining Spatial Association Rules for Composite Motif Discovery." In Mathematical Approaches to Polymer Sequence Analysis and Related Problems, 87–109. New York, NY: Springer New York, 2010. http://dx.doi.org/10.1007/978-1-4419-6800-5_5.

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Kitakami, Hajime, Tomoki Kanbara, Yasuma Mori, Susumu Kuroki, and Yukiko Yamazaki. "Modified PrefixSpan Method for Motif Discovery in Sequence Databases." In Lecture Notes in Computer Science, 482–91. Berlin, Heidelberg: Springer Berlin Heidelberg, 2002. http://dx.doi.org/10.1007/3-540-45683-x_52.

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Conference papers on the topic "Sequence motif"

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Chandar, V. Ravindra Krishna, and V. Sathiya Moorthi. "Sequence clustering using motif algorithm." In 2012 International Conference on Computer Communication and Informatics (ICCCI). IEEE, 2012. http://dx.doi.org/10.1109/iccci.2012.6158838.

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Yu, Qiang, Hongwei Huo, Ruixing Zhao, Dazheng Feng, Jeffrey Scott Vitter, and Jun Huan. "Reference sequence selection for motif searches." In 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE, 2015. http://dx.doi.org/10.1109/bibm.2015.7359745.

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PRAKASH, A., M. BLANCHETTE, S. SINHA, and M. TOMPA. "MOTIF DISCOVERY IN HETEROGENEOUS SEQUENCE DATA." In Proceedings of the Pacific Symposium. WORLD SCIENTIFIC, 2003. http://dx.doi.org/10.1142/9789812704856_0033.

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Ramanujam, E., and S. Padmavathi. "Constraint Frequent Motif Detection in sequence datasets." In 2012 Fourth International Conference on Advanced Computing (ICoAC). IEEE, 2012. http://dx.doi.org/10.1109/icoac.2012.6416844.

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Karaçalı, Bilge. "Hierarchical Motif Vectors for Amino Acid Sequence Alignment." In Biomedical Engineering. Calgary,AB,Canada: ACTAPRESS, 2012. http://dx.doi.org/10.2316/p.2012.764-055.

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Ng, Patrick, and Uri Keich. "Factoring local sequence composition in motif significance analysis." In Proceedings of the 19th International Conference. IMPERIAL COLLEGE PRESS, 2008. http://dx.doi.org/10.1142/9781848163324_0002.

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Sayed, Khaled, Nahed Solouma, and Yasser Kadah. "Yeast protein function motif extraction based on sequence alignment." In 2011 28th National Radio Science Conference (NRSC). IEEE, 2011. http://dx.doi.org/10.1109/nrsc.2011.5873650.

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Birch-Hirschfeld, Eckhard, Axel Walter, Anna Gabrielyan, Axel Stelzner, Hartmut Fritzsche, and Holger Schütz. "A new parallel triplex motif: sequence dependence of thermal stability." In XIth Symposium on Chemistry of Nucleic Acid Components. Prague: Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 1999. http://dx.doi.org/10.1135/css199902313.

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Gokalp, Osman. "DNA Sequence Motif Discovery Using Greedy Construction Algorithm Based Techniques." In 2020 5th International Conference on Computer Science and Engineering (UBMK). IEEE, 2020. http://dx.doi.org/10.1109/ubmk50275.2020.9219366.

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Li, Jiwei, Xianghua Zhang, Chun Yuan, Zhaohui Jiang, and Huanqing Feng. "Motif Extraction with Indicative Events for System Call Sequence Classification." In Fourth International Conference on Fuzzy Systems and Knowledge Discovery (FSKD 2007). IEEE, 2007. http://dx.doi.org/10.1109/fskd.2007.411.

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Reports on the topic "Sequence motif"

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Millan, Jose L. Sequence Motifs Specifying Homing and Metastasis to Bone. Fort Belvoir, VA: Defense Technical Information Center, July 2002. http://dx.doi.org/10.21236/ada407485.

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Yalovsky, Shaul, and Julian Schroeder. The function of protein farnesylation in early events of ABA signal transduction in stomatal guard cells of Arabidopsis. United States Department of Agriculture, January 2002. http://dx.doi.org/10.32747/2002.7695873.bard.

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Loss of function mutations in the farnesyltransferase β subunit gene ERA1 (enhanced response to abscisic acid), cause abscisic acid hypersensitivity in seedlings and in guard cells. This results in slowed water loss of plants in response to drought. Farnesyltransferase (PFT) catalyses the attachment of the 15-carbon isoprenoid farnesyl to conserved cysteine residues located in a conserved C-terminal domain designated CaaX box. PFT is a heterodimeric protein comprised of an a and b sununits. The a subunit is shared between PFT and geranylgeranyltransferase-I (PGGTI) which catalyses the attachem
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Yaron, Zvi, Abigail Elizur, Martin Schreibman, and Yonathan Zohar. Advancing Puberty in the Black Carp (Mylopharyngodon piceus) and the Striped Bass (Morone saxatilis). United States Department of Agriculture, January 2000. http://dx.doi.org/10.32747/2000.7695841.bard.

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Both the genes and cDNA sequences encoding the b-subunits of black carp LH and FSH were isolated, cloned and sequenced. Sequence analysis of the bcFSHb and LHb5'flanking regions revealed that the promoter region of both genes contains canonical TATA sequences, 30 bp and 17 bp upstream of the transcription start site of FSHb and LHb genes, respectively. In addition, they include several sequences of cis-acting motifs, required for inducible and tissue-specific transcriptional regulation: the gonadotropin-specific element (GSE), GnRH responsive element (GRE), half sites of estrogen and androgen
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Pawlowski, Wojtek P., and Avraham A. Levy. What shapes the crossover landscape in maize and wheat and how can we modify it. United States Department of Agriculture, January 2015. http://dx.doi.org/10.32747/2015.7600025.bard.

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Meiotic recombination is a process in which homologous chromosomes engage in the exchange of DNA segments, creating gametes with new genetic makeup and progeny with new traits. The genetic diversity generated in this way is the main engine of crop improvement in sexually reproducing plants. Understanding regulation of this process, particularly the regulation of the rate and location of recombination events, and devising ways of modifying them, was the major motivation of this project. The project was carried out in maize and wheat, two leading crops, in which any advance in the breeder’s tool
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Altstein, Miriam, and Ronald Nachman. Rationally designed insect neuropeptide agonists and antagonists: application for the characterization of the pyrokinin/Pban mechanisms of action in insects. United States Department of Agriculture, October 2006. http://dx.doi.org/10.32747/2006.7587235.bard.

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The general objective of this BARD project focused on rationally designed insect neuropeptide (NP) agonists and antagonists, their application for the characterization of the mechanisms of action of the pyrokinin/PBAN (PK-PBAN) family and the development of biostable, bioavailable versions that can provide the basis for development of novel, environmentally-friendly pest insect control agents. The specific objectives of the study, as originally proposed, were to: (i) Test stimulatory potencies of rationally designed backbone cyclic (BBC) peptides on pheromonotropic, melanotropic, myotropic and
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McElwain, Terry F., Eugene Pipano, Guy H. Palmer, Varda Shkap, Stephn A. Hines, and Wendy C. Brown. Protection of Cattle against Babesiosis: Immunization against Babesia bovis with an Optimized RAP-1/Apical Complex Construct. United States Department of Agriculture, September 1999. http://dx.doi.org/10.32747/1999.7573063.bard.

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Previous research and current efforts at control of babesiosis fall short of meeting the needs of countries where the disease is endemic, such as Israel, as well as the needs of exporting countries and countries bordering on endemic areas, such as the U.S. Our long-term goal is to develop improved methods of immunization against bovine babesiosis based on an understanding of the molecular mechanisms of immune protection and parasite targets of a protective immune response. In our previous BARD project, we established the basis for focusing on rhoptry antigens as components of a subunit vaccine
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Palmer, Guy, Varda Shkap, Wendy Brown, and Thea Molad. Control of bovine anaplasmosis: cytokine enhancement of vaccine efficacy. United States Department of Agriculture, March 2007. http://dx.doi.org/10.32747/2007.7695879.bard.

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Anaplasmosis an arthropod-born disease of cattle caused by the rickettsia Anaplasma marginale and is an impediment to efficient production of healthy livestock in both Israel and the United States. Currently the only effective vaccines are derived from the blood of infected cattle. The risk of widespread transmission of both known and newly emergent pathogens has prevented licensure of live blood-based vaccines in the U.S. and is a major concern for their continued use in Israel. Consequently development of a safe, effective vaccine is a high priority. In this collaborative project we focused
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