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Dissertations / Theses on the topic 'Sequence motif'

Author: Grafiati

Published: 4 June 2021

Last updated: 20 February 2023

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1

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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3

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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4

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

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5

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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6

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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7

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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8

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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9

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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10

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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Mak, Chi-ho. "Characterization of a recombination signal sequence and kappa-B motif DNA binding protein, KRc /." The Ohio State University, 1997. http://rave.ohiolink.edu/etdc/view?acc_num=osu148794334152931.

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12

Naik, Ashwini. "Mining Gene Regulatory Motifs Using the Concept of Sequence Coverage." Ohio University / OhioLINK, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=ohiou1408699463.

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Langer, Björn. "Phenotype-related regulatory element and transcription factor identification via phylogeny-aware discriminative sequence motif scoring." Doctoral thesis, Center for Systems Biology Dresden, 2017. https://tud.qucosa.de/id/qucosa%3A31172.

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Understanding the connection between an organism’s genotype and its phenotype is a key question in evolutionary biology and genetics. It has been shown that many changes of morphological or other complex phenotypic traits result from changes in the expression pattern of key developmental genes rather than from changes in the genes itself. Such altered gene expression arises often from changes in the gene regulatory regions. That usually means the loss of important transcription factor (TF) binding sites within these regulatory regions, because the interaction between TFs and specific sites on

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14

Choi, Hyunjin. "An Interdisciplinary Approach: Computational Sequence Motif Search and Prediction of Protein Function with Experimental Validation." Diss., Virginia Tech, 2013. http://hdl.handle.net/10919/51762.

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Pathogens colonize their hosts by releasing molecules that can enter host cells. A biotrophic oomycete plant pathogen, Phytophthora sojae harbors a superfamily of effector genes whose protein products enter the cells of the host, soybean. Many of the effectors contain an RXLR-dEER motif in their N-terminus. More than 400 members belonging to this family have been previously identified using a Hidden Markov Model. Amino acids flanking the RXLR motif have been utilized to identify effector proteins from the P. sojae secretome, despite the high level of sequence divergence among the members of

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15

McMillen, Lyle, and l. mcmillen@sct gu edu au. "Isolation and Characterisation of the 5'-Nucleotidase from Escherichia coli." Griffith University. School of Biomolecular and Biomedical Science, 2001. http://www4.gu.edu.au:8080/adt-root/public/adt-QGU20030226.153545.

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Escherichia coli 5'-nucleotidase is a periplasmically localised enzyme capable of hydrolysing a broad range of substrates, including all 5'-ribo- and 5'-deoxyribonucleotides, uridine diphosphate sugars, and a number of synthetic substrates such as bis (r-nitrophenyl) phosphate. The enzyme has been shown to contain at least one zinc ion following purification, and to have two metal binding sites in the catalytic cleft. 5'-Nucleotidase activity is significantly stimulated by the addition of particular divalent metal ions, most notably cobalt which results in a 30-50 fold increase in activity.

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16

McMillen, Lyle. "Isolation and Characterisation of the 5'-Nucleotidase from Escherichia coli." Thesis, Griffith University, 2001. http://hdl.handle.net/10072/366487.

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Escherichia coli 5'-nucleotidase is a periplasmically localised enzyme capable of hydrolysing a broad range of substrates, including all 5'-ribo- and 5'-deoxyribonucleotides, uridine diphosphate sugars, and a number of synthetic substrates such as bis (r-nitrophenyl) phosphate. The enzyme has been shown to contain at least one zinc ion following purification, and to have two metal binding sites in the catalytic cleft. 5'-Nucleotidase activity is significantly stimulated by the addition of particular divalent metal ions, most notably cobalt which results in a 30-50 fold increase in activity.

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17

Tang, Thomas Cheuk Kai. "Discovering Protein Sequence-Structure Motifs and Two Applications to Structural Prediction." Thesis, University of Waterloo, 2004. http://hdl.handle.net/10012/1188.

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This thesis investigates the correlations between short protein peptide sequences and local tertiary structures. In particular, it introduces a novel algorithm for partitioning short protein segments into clusters of local sequence-structure motifs, and demonstrates that these motif clusters contain useful structural information via two applications to structural prediction. The first application utilizes motif clusters to predict local protein tertiary structures. A novel dynamic programming algorithm that performs comparably with some of the best existing algorithms is describe

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18

Lombe, Chipampe Patricia. "Analysis, expression profiling and characterization of hsa-miR-5698 target genes as putative dynamic network biomarkers for prostate cancer: a combined in silico and molecular approach." University of the Western Cape, 2019. http://hdl.handle.net/11394/7026.

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Philosophiae Doctor - PhD<br>2018, the International Agency for Research on Cancer (IARC) estimated that prostate cancer (PCa) was the second leading cause of death in males worldwide. The number of deaths are expected to raise by 50 % in the next decade. This rise is attributed to the shortcomings of the current diagnostic, prognostic, and therapeutic biomarkers used in the management of the disease. Therefore, research into more sensitive, specific and effective biomarkers is a requirement. The use of biomarkers in PCa diagnosis and management takes advantage of the genetic alterations and a

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19

Pfeiffer, Philip Edward. "A System for Determining the Statistical Significance of the Frequency of Short DNA Motif Matches in a Genome - An Analytical Approach." University of Dayton / OhioLINK, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=dayton1304599225.

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20

Langer, Björn [Verfasser], Michael [Akademischer Betreuer] Hiller, Ivo [Gutachter] Sbalzarini, and Peter [Gutachter] Stadler. "Phenotype-related regulatory element and transcription factor identification via phylogeny-aware discriminative sequence motif scoring / Björn Langer ; Gutachter: Ivo Sbalzarini, Peter Stadler ; Betreuer: Michael Hiller." Dresden : Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2018. http://d-nb.info/1226813224/34.

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Langer, Björn [Verfasser], Michael [Akademischer Betreuer] Hiller, Ivo Fabian [Gutachter] Sbalzarini, and Peter [Gutachter] Stadler. "Phenotype-related regulatory element and transcription factor identification via phylogeny-aware discriminative sequence motif scoring / Björn Langer ; Gutachter: Ivo Sbalzarini, Peter Stadler ; Betreuer: Michael Hiller." Dresden : Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2018. http://d-nb.info/1226813224/34.

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22

Bellora, Pereyra Nicolás. "In silico analysis of regulatory motifs in gene promoters." Doctoral thesis, Universitat Pompeu Fabra, 2010. http://hdl.handle.net/10803/7202.

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Regulation of gene transcription is a complex process involving many different proteins, some of which bind in a sequence-specific manner to DNA motifs in the gene promoter. The need to maintain specific interactions between transcription factors and proteins involved in the RNA polymerase II complex is expected to impose constrains on the relative position and spacing of the interacting DNA motifs. The present work includes the development of a novel approach to identify motifs that show a preferential location in DNA sequences and the implementation of a public web application called PEAKS.

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23

Zhong, Wei. "Clustering System and Clustering Support Vector Machine for Local Protein Structure Prediction." Digital Archive @ GSU, 2006. http://digitalarchive.gsu.edu/cs_diss/7.

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Protein tertiary structure plays a very important role in determining its possible functional sites and chemical interactions with other related proteins. Experimental methods to determine protein structure are time consuming and expensive. As a result, the gap between protein sequence and its structure has widened substantially due to the high throughput sequencing techniques. Problems of experimental methods motivate us to develop the computational algorithms for protein structure prediction. In this work, the clustering system is used to predict local protein structure. At first, recurring

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24

Sandve, Geir Kjetil. "Motif discovery in biological sequences." Thesis, Norwegian University of Science and Technology, Department of Computer and Information Science, 2005. http://urn.kb.se/resolve?urn=urn:nbn:no:ntnu:diva-9270.

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<p>This master thesis is a Ph.D. research plan for motif discovery in biological sequences, and consists of three main parts. Chapter 2 is a survey of methods for motif discovery in DNA regulatory regions, with a special emphasis on computational models. The survey presents an integrated model of the problem that allows systematic and coherent treatment of the surveyed methods. Chapter 3 presents a new algorithm for composite motif discovery in biological sequences. This algorithm has been used with success for motif discovery in protein sequences, and will in future work be extended on to

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25

Těthal, Jiří. "Fuzzy klasifikace DNA sekvencí." Master's thesis, Vysoké učení technické v Brně. Fakulta elektrotechniky a komunikačních technologií, 2013. http://www.nusl.cz/ntk/nusl-220008.

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The work deals with the fuzzy classification of DNA sequences. In the first part the theory summarized information about Fuzzy logic and methods of its use in the classification of biological sequence data. The second part is practically deal with the classification algorithm for assessing the similarity of sequences. Specifically, the dividing of coding and non-coding parts of the sequence and the use of fuzzy classification in DNA barcoding.

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26

Morozov, Vyacheslav. "Computational Methods for Inferring Transcription Factor Binding Sites." Thèse, Université d'Ottawa / University of Ottawa, 2012. http://hdl.handle.net/10393/23382.

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Position weight matrices (PWMs) have become a tool of choice for the identification of transcription factor binding sites in DNA sequences. PWMs are compiled from experimentally verified and aligned binding sequences. PWMs are then used to computationally discover novel putative binding sites for a given protein. DNA-binding proteins often show degeneracy in their binding requirement, the overall binding specificity of many proteins is unknown and remains an active area of research. Although PWMs are more reliable predictors than consensus string matching, they generally result in a high numb

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27

Roll, James Elwood. "Inferring RNA 3D Motifs from Sequence." Bowling Green State University / OhioLINK, 2019. http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1557482505513958.

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28

Soni, Neha. "Sequence motifs predictive of tissue-specific skipping." Thesis, Massachusetts Institute of Technology, 2006. http://hdl.handle.net/1721.1/35608.

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Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2006.<br>Includes bibliographical references (p. 53-55).<br>Alternative splicing plays a major role in protein diversity and regulating gene expression. Motifs that regulate tissue-specific alternative splicing have been identified by groups studying small sets of genes. We introduce a tissue-specific skipping score for skipped exons using exon-exon junction microarray data. We compare these exons with known literature-verified EST skipped exons and exons predicted to be skipped in both

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29

Lancaster, Owen. "Sequence and structural templates for protein motifs." Thesis, University of Manchester, 2006. http://www.manchester.ac.uk/escholar/uk-ac-man-scw:157940.

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Current methodologies for recognizing similar protein motifs are predominantly based upon establishing a homology relationship between the sequences. These methods are widely exploited to annotate new genomes and assign putative functions to new genes. However they are usually based on sequence data alone. More recent approaches have incorporated structural data into methods to improve the predictions compared to just sequence based methods alone. So far these approaches have not been widely exploited in bioinformatics for identifying common, small motifs. A test system was examined containing

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30

Buchholz, Frank, Anja Nitzsche, Maciej Paszkowski-Rogacz, Filomena Matarese, Eva M. Janssen-Megens, Nina C. Hubner, Herbert Schulz, et al. "RAD21 Cooperates with Pluripotency Transcription Factors in the Maintenance of Embryonic Stem Cell Identity." Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2016. http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-191596.

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For self-renewal, embryonic stem cells (ESCs) require the expression of specific transcription factors accompanied by a particular chromosome organization to maintain a balance between pluripotency and the capacity for rapid differentiation. However, how transcriptional regulation is linked to chromosome organization in ESCs is not well understood. Here we show that the cohesin component RAD21 exhibits a functional role in maintaining ESC identity through association with the pluripotency transcriptional network. ChIP-seq analyses of RAD21 reveal an ESC specific cohesin binding pattern that is

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31

Kopp, Wolfgang [Verfasser]. "Statistical methods for motif hit enrichment in DNA sequences / Wolfgang Kopp." Berlin : Freie Universität Berlin, 2017. http://d-nb.info/1135184852/34.

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32

Valebjørg, Vetle Søraas. "Discovery of approximate composite motifs in biological sequences." Thesis, Norwegian University of Science and Technology, Department of Computer and Information Science, 2006. http://urn.kb.se/resolve?urn=urn:nbn:no:ntnu:diva-10130.

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<p>Mapping the regulatory system in living organisms is a great challenge, and many methods have been created during the last 15 years to solve this problem. The biological processes are however more flexible and complex than first thought, and many of the methods lack the ability to imitate this exactly. The new method devised here is not a complete solution to this situation, but pose an innovative solution for finding approximate composite patterns in a set of sequences. Motifs are read from any third-party tool represented as either {A,C,G,T}, IUPAC or PWMs, and weighted with significance

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33

Holm, Lotta. "The MHC-glycopeptide-T cell interaction in collagen induced arthritis : a study using glycopeptides, isosteres and statistical molecular design in a mouse model for rheumatoid arthritis." Doctoral thesis, Umeå : Department of Chemistry, Umeå University, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-899.

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34

Buchholz, Frank, Anja Nitzsche, Maciej Paszkowski-Rogacz, Filomena Matarese, Eva M. Janssen-Megens, Nina C. Hubner, Herbert Schulz, et al. "RAD21 Cooperates with Pluripotency Transcription Factors in the Maintenance of Embryonic Stem Cell Identity." Public Library of Science, 2011. https://tud.qucosa.de/id/qucosa%3A29134.

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For self-renewal, embryonic stem cells (ESCs) require the expression of specific transcription factors accompanied by a particular chromosome organization to maintain a balance between pluripotency and the capacity for rapid differentiation. However, how transcriptional regulation is linked to chromosome organization in ESCs is not well understood. Here we show that the cohesin component RAD21 exhibits a functional role in maintaining ESC identity through association with the pluripotency transcriptional network. ChIP-seq analyses of RAD21 reveal an ESC specific cohesin binding pattern that is

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35

Sarver, Michael. "STRUCTURE-BASED MULTIPLE RNA SEQUENCE ALIGNMENT AND FINDING RNA MOTIFS." Bowling Green State University / OhioLINK, 2006. http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1151076710.

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36

El, Soufi Karim. "Study of circular code motifs in nucleic acid sequences." Thesis, Strasbourg, 2017. http://www.theses.fr/2017STRAD004/document.

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Le travail effectué dans cette thèse présente une nouvelle approche de la théorie du code circulaire dans les gènes qui a été initiée en 1996. Cette approche consiste à analyser les motifs construits à partir de ce code circulaire, ces motifs particuliers sont appelés motifs de code circulaire. Ainsi, nous avons développé des algorithmes de recherche pour localiser les motifs de code circulaire dans les séquences d'acides nucléiques afin de leur trouver une signification bioinformatique. En effet, le code circulaire X identifie dans les gènes est un ensemble de trinucleotides qui a la propriét

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37

Crowley, Louis J. "Structure-function studies of conserved sequence motifs of cytochrome b5 reductase." [Tampa, Fla] : University of South Florida, 2007. http://purl.fcla.edu/usf/dc/et/SFE0001913.

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38

Hicks, Matthew Raymond. "Coiled-coil assembly by proteins and peptides with unusual sequence motifs." Thesis, University of Sussex, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.311349.

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39

EL, MABROUK NADIA. "Recherche approchee de motifs - application a des sequences biologiques structurees." Paris 7, 1996. http://www.theses.fr/1996PA077199.

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Ce travail presente differentes methodes pour la recherche approchee, a erreurs pres, d'un motif p dans un texte t. Les erreurs considerees sont les substitutions de caracteres et les motifs sont, soit un mot, soit une classe de mots sur un alphabet. Deux des approches les plus efficaces, en theorie et en pratique, pour la recherche approchee sont les approches de type numerique qui se basent sur la manipulation de mots machine, et les approches de type boyer-moore. Nous avons concu une nouvelle methode de recherche qui tire profit, a la fois de l'efficacite de la demarche boyer-moore, et de l

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40

Liu, Kai. "Detecting stochastic motifs in network and sequence data for human behavior analysis." HKBU Institutional Repository, 2014. https://repository.hkbu.edu.hk/etd_oa/60.

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With the recent advent of Web 2.0, mobile computing, and pervasive sensing technologies, human activities can readily be logged, leaving digital traces of di.erent forms. For instance, human communication activities recorded in online social networks allow user interactions to be represented as “network” data. Also, human daily activities can be tracked in a smart house, where the log of sensor triggering events can be represented as “sequence” data. This thesis research aims to develop computational data mining algorithms using the generative modeling approach to extract salient patterns (mot

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41

John, Rosalind. "Identification of potential gene coding sequences within large cloned DNA arrays : analysis of zinc finger motif." Thesis, Imperial College London, 1991. http://hdl.handle.net/10044/1/46844.

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42

Sinoquet, Christine. "Grammaires a transformations morphiques recherche de motif - exacte ou approchee - adaptee aux sequences genetiques : le systeme gtm." Rennes 1, 1998. http://www.theses.fr/1998REN10048.

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Nous nous interessons a la recherche de motifs composes dans une sequence. Ces motifs sont decrits a l'aide de grammaires a variables de type chaine et a transformations morphiques. Le concept de transformation morphique permet de capturer les aspects hors-contexte (inversion) et contextuel (repetition) d'un langage de sequences donne. Il est adapte a la description de liens entre regions d'une sequence et en particulier a la modelisation des dependances intra-moleculaires qui etablissent la structure secondaire des sequences genetiques. Nous definissons une classe de grammaires discontinues (

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43

Roth, Christian [Verfasser]. "Statistical methods for biological sequence analysis for DNA binding motifs and protein contacts / Christian Roth." Göttingen : Niedersächsische Staats- und Universitätsbibliothek Göttingen, 2021. http://nbn-resolving.de/urn:nbn:de:gbv:7-21.11130/00-1735-0000-0008-5912-0-2.

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44

Prytuliak, Roman [Verfasser], and Christian [Akademischer Betreuer] Leibold. "Recognition of short functional motifs in protein sequences / Roman Prytuliak ; Betreuer: Christian Leibold." München : Universitätsbibliothek der Ludwig-Maximilians-Universität, 2018. http://d-nb.info/1166559513/34.

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Crowley, Louis J. "Structure-Function Studies of Conserved Sequence Motifs of Cytochrome b₅ Reductase:." Scholar Commons, 2007. https://scholarcommons.usf.edu/etd/682.

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NADH:Cytochrome b5 Reductase (cb5r) catalyzes the two electron reduction of the iron center of the heme cofactor found within cytochrome b5 (cb5) utilizing reducing equivalents of the nicotinamide adenine dinucleotide (NADH) coenzyme. Cb5r is characterized by two domains necessary for proper enzyme function: a flavin-binding domain and a pyridine nucleotide-binding domain. Within these domains are highly conserved "motifs" necessary for the proper binding and orientation of both the NADH coenzyme and the FAD cofactor. To address the importance of these conserved motifs site-directed mutagenesi

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Jorda, Julien. "Analyse systématique des motifs répétés en tandem dans les séquences protéiques." Thesis, Montpellier 2, 2010. http://www.theses.fr/2010MON20090/document.

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Au cours des dernières décennies, les avancées techniques dans la biologie moléculaire telles que les projets de séquençage de génome ont eu pour conséquence un accroissement du volume des banques de données biologiques. Parmi ces données, des séquences présentent des motifs similaires entre eux, répétés de façon juxtaposée, appelés répétitions en tandem. L'objectif de cette thèse est de comprendre l'existence de ces répétitions dans les séquences protéiques via une analyse à grande échelle<br>Over the last decades, technical advances in molecular biology such as the genome sequencing projects

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47

Sanghvi, Jubin Dinakarpandian Deendayal. "IFREE - an Indexed Forest of Representer Expressions Extractor for position frequency matrices to rapidly detect sequence motifs." Diss., UMK access, 2006.

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Thesis (M.S.)--School of Computing and Engineering. University of Missouri--Kansas City, 2006.<br>"A thesis in computer science." Typescript. Advisor: Deendayal Dinakarpandian. Vita. Title from "catalog record" of the print edition Description based on contents viewed Jan. 29, 2007. Includes bibliographical references (leaves 60-62). Online version of the print edition.

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Pham, Quang-Khai. "Time Sequence Summarization: Theory and Applications." Phd thesis, Université de Nantes, 2010. http://tel.archives-ouvertes.fr/tel-00538512.

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Les domaines de la médecine, du web, du commerce ou de la nance génèrent et stockent de grandes masses d'information sous la forme de séquences d'événements. Ces archives représentent des sources d'information très riches pour des analystes avides d'y découvrir des perles de connaissance. Par exemple, les biologistes cherchent à découvrir les facteurs de risque d'une maladie en analysant l'historique des patients, les producteurs de contenu web et les bureaux de marketing examinent les habitudes de consommation des clients et les opérateurs boursiers suivent les évolutions du marché pour mieux

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Grunert, Steffen. "Strukturelles und funktionelles Verständnis von Membranproteinen im Kontext sequenzmotivbasierter Methoden." Doctoral thesis, Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2017. http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-229383.

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Die vorliegende Arbeit wurde im Rahmen einer kooperativen Promotion zwischen der TU Dresden und der Hochschule Mittweida angefertigt. In dieser werden neuartige, computerorientierte Ansätze für die Analyse von Membranproteinen vorgestellt. Membranproteine sind von essentieller Bedeutung für eine Vielzahl biologischer Prozesse innerhalb eines Organismus und stellen wichtige Zielmoleküle für eine breite Palette von Pharmazeutika dar. Ihre Sequenzen liefern wertvolle und teilweise noch nicht entschlüsselte Informationen über die dreidimensionale Struktur und funktionale Eigenschaften. Innerhalb d

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Liang, Chengzhi. "COPIA: A New Software for Finding Consensus Patterns in Unaligned Protein Sequences." Thesis, University of Waterloo, 2001. http://hdl.handle.net/10012/1050.

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Abstract:

Consensus pattern problem (CPP) aims at finding conserved regions, or motifs, in unaligned sequences. This problem is NP-hard under various scoring schemes. To solve this problem for protein sequences more efficiently,a new scoring scheme and a randomized algorithm based on substitution matrix are proposed here. Any practical solutions to a bioinformatics problem must observe twoprinciples: (1) the problem that it solves accurately describes the real problem; in CPP, this requires the scoring scheme be able to distinguisha real motif from background; (2) it provides an efficient algorithmt

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