Algorithms on Strings Trees and Sequences

Author: Dan Gusfield
Publisher: Cambridge University Press
ISBN: 9780521585194
Format: PDF, Docs
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String algorithms are a traditional area of study in computer science. In recent years their importance has grown dramatically with the huge increase of electronically stored text and of molecular sequence data (DNA or protein sequences) produced by various genome projects. This 1997 book is a general text on computer algorithms for string processing. In addition to pure computer science, the book contains extensive discussions on biological problems that are cast as string problems, and on methods developed to solve them. It emphasises the fundamental ideas and techniques central to today's applications. New approaches to this complex material simplify methods that up to now have been for the specialist alone. With over 400 exercises to reinforce the material and develop additional topics, the book is suitable as a text for graduate or advanced undergraduate students in computer science, computational biology, or bio-informatics. Its discussion of current algorithms and techniques also makes it a reference for professionals.

Theoretical Computer Science

Author: Mario Coppo
Publisher: Springer Science & Business Media
ISBN: 9783540291060
Format: PDF, ePub, Mobi
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This book constitutes the refereed proceedings of the 9th International Conference on Theoretical Computer Science, ICTCS 2005, held at the Certosa di Pontignano, Siena, Italy, in October 2005. The 29 revised full papers presented together with an invited paper and abstracts of 2 invited talks were carefully reviewed and selected from 83 submissions. The papers address all current issues in theoretical computer science and focus especially on analysis and design of algorithms, computability, computational complexity, cryptography, formal languages and automata, foundations of programming languages and program analysis, natural computing paradigms (quantum computing, bioinformatics), program specification and verification, term rewriting, theory of logical design and layout, type theory, security, and symbolic and algebraic computation.

Combinatorial Pattern Matching Algorithms in Computational Biology Using Perl and R

Author: Gabriel Valiente
Publisher: CRC Press
ISBN: 9781420069747
Format: PDF
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Emphasizing the search for patterns within and between biological sequences, trees, and graphs, Combinatorial Pattern Matching Algorithms in Computational Biology Using Perl and R shows how combinatorial pattern matching algorithms can solve computational biology problems that arise in the analysis of genomic, transcriptomic, proteomic, metabolomic, and interactomic data. It implements the algorithms in Perl and R, two widely used scripting languages in computational biology. The book provides a well-rounded explanation of traditional issues as well as an up-to-date account of more recent developments, such as graph similarity and search. It is organized around the specific algorithmic problems that arise when dealing with structures that are commonly found in computational biology, including biological sequences, trees, and graphs. For each of these structures, the author makes a clear distinction between problems that arise in the analysis of one structure and in the comparative analysis of two or more structures. He also presents phylogenetic trees and networks as examples of trees and graphs in computational biology. This book supplies a comprehensive view of the whole field of combinatorial pattern matching from a computational biology perspective. Along with thorough discussions of each biological problem, it includes detailed algorithmic solutions in pseudo-code, full Perl and R implementation, and pointers to other software, such as those on CPAN and CRAN.

Grundlegende Algorithmen

Author: Volker Heun
Publisher: Springer-Verlag
ISBN: 3322803236
Format: PDF
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Jeder Student IT-naher Studiengänge benötigt Grundkenntnisse im Bereich Algorithmen. Lernen Sie anhand alltäglicher Aufgabenstellungen aus der Informatik die richtigen Algorithmen einzusetzen. Sie werden auch die dahinter steckenden, allgemein anwendbaren Entwurfsmethoden sowie die grundlegenden Techniken zur Analyse verstehen und anwenden können.

Hidden Markov Models for Bioinformatics

Author: T. Koski
Publisher: Springer Science & Business Media
ISBN: 9781402001369
Format: PDF, ePub, Mobi
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The purpose of this book is to give a thorough and systematic introduction to probabilistic modeling in bioinformatics. The book contains a mathematically strict and extensive presentation of the kind of probabilistic models that have turned out to be useful in genome analysis. Questions of parametric inference, selection between model families, and various architectures are treated. Several examples are given of known architectures (e.g., profile HMM) used in genome analysis. Audience: This book will be of interest to advanced undergraduate and graduate students with a fairly limited background in probability theory, but otherwise well trained in mathematics and already familiar with at least some of the techniques of algorithmic sequence analysis.

Algorithmen Eine Einf hrung

Author: Thomas H. Cormen
Publisher: Walter de Gruyter GmbH & Co KG
ISBN: 3110522012
Format: PDF, ePub
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Der "Cormen" bietet eine umfassende und vielseitige Einführung in das moderne Studium von Algorithmen. Es stellt viele Algorithmen Schritt für Schritt vor, behandelt sie detailliert und macht deren Entwurf und deren Analyse allen Leserschichten zugänglich. Sorgfältige Erklärungen zur notwendigen Mathematik helfen, die Analyse der Algorithmen zu verstehen. Den Autoren ist es dabei geglückt, Erklärungen elementar zu halten, ohne auf Tiefe oder mathematische Exaktheit zu verzichten. Jedes der weitgehend eigenständig gestalteten Kapitel stellt einen Algorithmus, eine Entwurfstechnik, ein Anwendungsgebiet oder ein verwandtes Thema vor. Algorithmen werden beschrieben und in Pseudocode entworfen, der für jeden lesbar sein sollte, der schon selbst ein wenig programmiert hat. Zahlreiche Abbildungen verdeutlichen, wie die Algorithmen arbeiten. Ebenfalls angesprochen werden Belange der Implementierung und andere technische Fragen, wobei, da Effizienz als Entwurfskriterium betont wird, die Ausführungen eine sorgfältige Analyse der Laufzeiten der Programme mit ein schließen. Über 1000 Übungen und Problemstellungen und ein umfangreiches Quellen- und Literaturverzeichnis komplettieren das Lehrbuch, dass durch das ganze Studium, aber auch noch danach als mathematisches Nachschlagewerk oder als technisches Handbuch nützlich ist. Für die dritte Auflage wurde das gesamte Buch aktualisiert. Die Änderungen sind vielfältig und umfassen insbesondere neue Kapitel, überarbeiteten Pseudocode, didaktische Verbesserungen und einen lebhafteren Schreibstil. So wurden etwa - neue Kapitel zu van-Emde-Boas-Bäume und mehrfädigen (engl.: multithreaded) Algorithmen aufgenommen, - das Kapitel zu Rekursionsgleichungen überarbeitet, sodass es nunmehr die Teile-und-Beherrsche-Methode besser abdeckt, - die Betrachtungen zu dynamischer Programmierung und Greedy-Algorithmen überarbeitet; Memoisation und der Begriff des Teilproblem-Graphen als eine Möglichkeit, die Laufzeit eines auf dynamischer Programmierung beruhender Algorithmus zu verstehen, werden eingeführt. - 100 neue Übungsaufgaben und 28 neue Problemstellungen ergänzt. Umfangreiches Dozentenmaterial (auf englisch) ist über die Website des US-Verlags verfügbar.

String Processing and Information Retrieval

Author: Edleno Moura
Publisher: Springer
ISBN: 3319119184
Format: PDF
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This book constitutes the proceedings of the 21st International Symposium on String Processing and Information Retrieval, SPIRE 2014, held in Ouro Preto, Brazil, in October 2014. The 20 full and 6 short papers included in this volume were carefully reviewed and selected from 45 submissions. The papers focus not only on fundamental algorithms in string processing and information retrieval, but address also application areas such as computational biology, Web mining and recommender systems. They are organized in topical sections on compression, indexing, genome and related topics, sequences and strings, search, as well as on mining and recommending.

Sequence Evolution Function

Author: Eugene Koonin
Publisher: Springer Science & Business Media
ISBN: 9781402072741
Format: PDF, Kindle
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Sequence - Evolution - Function is an introduction to the computational approaches that play a critical role in the emerging new branch of biology known as functional genomics. The book provides the reader with an understanding of the principles and approaches of functional genomics and of the potential and limitations of computational and experimental approaches to genome analysis. Sequence - Evolution - Function should help bridge the "digital divide" between biologists and computer scientists, allowing biologists to better grasp the peculiarities of the emerging field of Genome Biology and to learn how to benefit from the enormous amount of sequence data available in the public databases. The book is non-technical with respect to the computer methods for genome analysis and discusses these methods from the user's viewpoint, without addressing mathematical and algorithmic details. Prior practical familiarity with the basic methods for sequence analysis is a major advantage, but a reader without such experience will be able to use the book as an introduction to these methods. This book is perfect for introductory level courses in computational methods for comparative and functional genomics.

Data Mining in Bioinformatics

Author: Jason T. L. Wang
Publisher: Springer Science & Business Media
ISBN: 1846280591
Format: PDF, Docs
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Written especially for computer scientists, all necessary biology is explained. Presents new techniques on gene expression data mining, gene mapping for disease detection, and phylogenetic knowledge discovery.