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Biology --- Sequence alignment (Bioinformatics) --- Data processing. --- Alignment, Sequence (Bioinformatics) --- Determination, Sequence homology (Bioinformatics) --- Homology determination, Sequence (Bioinformatics) --- Sequence homology determination (Bioinformatics) --- Genetics --- Amino acid sequence --- Nucleotide sequence --- Technique --- Bioinformàtica --- Processament de dades

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This textbook provides step-by-step protocols and detailed explanations for RNA Sequencing, ChIP-Sequencing and Epigenetic Sequencing applications. The reader learns how to perform Next Generation Sequencing data analysis, how to interpret and visualize the data, and acquires knowledge on the statistical background of the used software tools. Written for biomedical scientists and medical students, this textbook enables the end user to perform and comprehend various Next Generation Sequencing applications and their analytics without prior understanding in bioinformatics or computer sciences.

Genetics. --- Bioinformatics. --- Medicine. --- Genetics and Genomics. --- Biomedicine, general. --- Health Workforce --- Bio-informatics --- Biological informatics --- Biology --- Information science --- Computational biology --- Systems biology --- Embryology --- Mendel's law --- Adaptation (Biology) --- Breeding --- Chromosomes --- Heredity --- Mutation (Biology) --- Variation (Biology) --- Data processing --- Sequence alignment (Bioinformatics) --- Alignment, Sequence (Bioinformatics) --- Determination, Sequence homology (Bioinformatics) --- Homology determination, Sequence (Bioinformatics) --- Sequence homology determination (Bioinformatics) --- Genetics --- Amino acid sequence --- Nucleotide sequence --- Technique --- Biologia computacional --- Biologia --- Biologia de sistemes --- Neurociència computacional --- Bioinformàtica

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This book develops a new approach called parameter advising for finding a parameter setting for a sequence aligner that yields a quality alignment of a given set of input sequences. In this framework, a parameter advisor is a procedure that automatically chooses a parameter setting for the input, and has two main ingredients: (a)         the set of parameter choices considered by the advisor, and (b)         an estimator of alignment accuracy used to rank alignments produced by the aligner. On coupling a parameter advisor with an aligner, once the advisor is trained in a learning phase, the user simply inputs sequences to align, and receives an output alignment from the aligner, where the advisor has automatically selected the parameter setting. The chapters first lay out the foundations of parameter advising, and then cover applications and extensions of advising. The content •   examines formulations of parameter advising and their computational complexity, •   develops methods for learning good accuracy estimators, •   presents approximation algorithms for finding good sets of parameter choices, and •   assesses software implementations of advising that perform well on real biological data. Also explored are applications of parameter advising to •   adaptive local realignment, where advising is performed on local regions of the sequences to automatically adapt to varying mutation rates, and •   ensemble alignment, where advising is applied to an ensemble of aligners to effectively yield a new aligner of higher quality than the individual aligners in the ensemble. The book concludes by offering future directions in advising research.

Sequence alignment (Bioinformatics) --- Computer science. --- Algorithms. --- Bioinformatics. --- Mathematical optimization. --- Computer Science. --- Computational Biology/Bioinformatics. --- Algorithm Analysis and Problem Complexity. --- Discrete Optimization. --- Alignment, Sequence (Bioinformatics) --- Determination, Sequence homology (Bioinformatics) --- Homology determination, Sequence (Bioinformatics) --- Sequence homology determination (Bioinformatics) --- Genetics --- Amino acid sequence --- Nucleotide sequence --- Technique --- Computer software. --- Algorism --- Algebra --- Arithmetic --- Software, Computer --- Computer systems --- Bio-informatics --- Biological informatics --- Biology --- Information science --- Computational biology --- Systems biology --- Foundations --- Data processing --- Optimization (Mathematics) --- Optimization techniques --- Optimization theory --- Systems optimization --- Mathematical analysis --- Maxima and minima --- Operations research --- Simulation methods --- System analysis

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From basic performing of sequence alignment through a proficiency at understanding how most industry-standard alignment algorithms achieve their results, Multiple Sequence Alignment Methods describes numerous algorithms and their nuances in chapters written by the experts who developed these algorithms.  The various multiple sequence alignment algorithms presented in this handbook give a flavor of the broad range of choices available for multiple sequence alignment generation, and their diversity is a clear reflection of the complexity of the multiple sequence alignment problem and the amount of information that can be obtained from multiple sequence alignments.  Each of these chapters not only describes the algorithm it covers but also presents instructions and tips on using their implementation, as is fitting with its inclusion in the highly successful Methods in Molecular Biology series.   Authoritative and practical, Multiple Sequence Alignment Methods provides a readily available resource which will allow practitioners to experiment with different algorithms and find the particular algorithm that is of most use in their application.

Sequence alignment (Bioinformatics) --- Computational biology --- Publication Formats --- Genetic Techniques --- Biology --- Databases, Genetic --- Investigative Techniques --- Databases, Factual --- Biological Science Disciplines --- Publication Characteristics --- Analytical, Diagnostic and Therapeutic Techniques and Equipment --- Databases as Topic --- Natural Science Disciplines --- Information Systems --- Disciplines and Occupations --- Information Storage and Retrieval --- Medical Informatics Applications --- Information Science --- Medical Informatics --- Sequence Alignment --- Databases, Protein --- Methods --- Computational Biology --- Handbooks --- Health & Biological Sciences --- Biology - General --- Computational biology. --- methods --- Methodological Studies --- Methodological Study --- Procedures --- Studies, Methodological --- Study, Methodological --- Method --- Procedure --- Protein Structure Databases --- SwissProt --- Amino Acid Sequence Databases --- Databases, 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Systems --- Data Systems --- Emergency Care Information Systems --- Information Retrieval Systems --- Ancillary Information System --- Data System --- Information Retrieval System --- Information System --- Information System, Ancillary --- Information Systems, Ancillary --- System, Ancillary Information --- System, Data --- System, Information --- System, Information Retrieval --- Systems, Ancillary Information --- Systems, Data --- Systems, Information --- Systems, Information Retrieval --- Natural Sciences --- Physical Sciences --- Discipline, Natural Science --- Disciplines, Natural Science --- Natural Science --- Natural Science Discipline --- Physical Science --- Science, Natural --- Science, Physical --- Sciences, Natural --- Sciences, Physical --- Data Banks as Topic --- Data Bases as Topic --- Databanks as Topic --- Biologic Sciences --- Biological Science --- Science, Biological --- Sciences, Biological --- Biological Sciences --- Life Sciences --- Biologic Science --- Biological Science Discipline --- Discipline, Biological Science --- Disciplines, Biological Science --- Life Science --- Science Discipline, Biological --- Science Disciplines, Biological --- Science, Biologic --- Science, Life --- Sciences, Biologic --- Sciences, Life --- Data Banks, Factual --- Data Bases, Factual --- Databanks, Factual --- Data Bank, Factual --- Data Base, Factual --- Databank, Factual --- Database, Factual --- Factual Data Bank --- Factual Data Banks --- Factual Data Base --- Factual Data Bases --- Factual Databank --- Factual Databanks --- Factual Database --- Factual Databases --- Investigative Technics --- Investigative Technic --- Investigative Technique --- Technic, Investigative --- Technics, Investigative --- Technique, Investigative --- Techniques, Investigative --- Genetic Data Banks --- Genetic Data Bases --- Genetic Databanks --- Genetic Information Databases --- Genetic Databases --- Genetic Sequence Databases --- OMIM --- Online Mendelian Inheritance In Man --- Bank, Genetic Data --- Banks, Genetic Data --- Data Bank, Genetic --- Data Banks, Genetic --- Data Base, Genetic --- Data Bases, Genetic --- Databank, Genetic --- Databanks, Genetic --- Database, Genetic --- Database, Genetic Information --- Database, Genetic Sequence --- Databases, Genetic Information --- Databases, Genetic Sequence --- Genetic Data Bank --- Genetic Data Base --- Genetic Databank --- Genetic Database --- Genetic Information Database --- Genetic Sequence Database --- Information Database, Genetic --- Information Databases, Genetic --- Sequence Database, Genetic --- Sequence Databases, Genetic --- Genetic Technic --- Genetic Technics --- Genetic Technique --- Technic, Genetic --- Technics, Genetic --- Technique, Genetic --- Techniques, Genetic --- Genetics --- Alignment, Sequence (Bioinformatics) --- Determination, Sequence homology (Bioinformatics) --- Homology determination, Sequence (Bioinformatics) --- Sequence homology determination (Bioinformatics) --- Bio-Informatics --- Biology, Computational --- Computational Molecular Biology --- Bioinformatics --- Molecular Biology, Computational --- Bio Informatics --- Bio-Informatic --- Bioinformatic --- Biologies, Computational Molecular --- Biology, Computational Molecular --- Computational Molecular Biologies --- Molecular Biologies, Computational --- Life sciences. --- Bioinformatics. --- Life Sciences. --- Bio-informatics --- Biological informatics --- Information science --- Systems biology --- Biosciences --- Science --- Data processing

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The storage, processing, description, transmission, connection, and analysis of the waves of new genomic data have made bioinformatics skills essential for scientists working with DNA sequences. In Bioinformatics for DNA Sequence Analysis, experts in the field provide practical guidance and troubleshooting advice for the computational analysis of DNA sequences, covering a range of issues and methods that unveil the multitude of applications and the vital relevance that the use of bioinformatics has today. Individual book chapters explore the use of specific bioinformatic tools, accompanied by practical examples, a discussion on the interpretation of results, and specific comments on strengths and limitations of the methods and tools. As a part of the highly successful Methods in Molecular Biology™ series, this work provides the kind of detailed description and implementation advice that is crucial for getting optimal results. Focused and cutting-edge, Bioinformatics for DNA Sequence Analysis serves molecular biologists, geneticists, and biochemists as an enriched task-oriented manual, offering step-by-step guidance for the analysis of DNA sequences in a simple but meaningful fashion.

Sequence Analysis, DNA --- Computational Biology --- Bioinformatics --- Nucleotide sequence --- Bio-informatique --- Génome humain --- methods --- Laboratory manuals --- Manuels de laboratoire --- Séquençage --- Methods --- Biology --- Sequence Analysis --- Investigative Techniques --- Genetic Techniques --- Analytical, Diagnostic and Therapeutic Techniques and Equipment --- Biological Science Disciplines --- Natural Science Disciplines --- Disciplines and Occupations --- Biology - General --- Health & Biological Sciences --- Génome humain --- Séquençage --- Analysis, Sequence --- Determination, Sequence --- Determinations, Sequence --- Sequence Determinations --- Sequence Determination --- Analyses, Sequence --- Sequence Analyses --- Bio-Informatics --- Biology, Computational --- Computational Molecular Biology --- Molecular Biology, Computational --- Bio Informatics --- Bio-Informatic --- Bioinformatic --- Biologies, Computational Molecular --- Biology, Computational Molecular --- Computational Molecular Biologies --- Molecular Biologies, Computational --- Natural Sciences --- Physical Sciences --- Discipline, Natural Science --- Disciplines, Natural Science --- Natural Science --- Natural Science Discipline --- Physical Science --- Science, Natural --- Science, Physical --- Sciences, Natural --- Sciences, Physical --- Biologic Sciences --- Biological Science --- Science, Biological --- Sciences, Biological --- Biological Sciences --- Life Sciences --- Biologic Science --- Biological Science Discipline --- Discipline, Biological Science --- Disciplines, Biological Science --- Life Science --- Science Discipline, Biological --- Science Disciplines, Biological --- Science, Biologic --- Science, Life --- Sciences, Biologic --- Sciences, Life --- Genetic Technic --- Genetic Technics --- Genetic Technique --- Technic, Genetic --- Technics, Genetic --- Technique, Genetic --- Techniques, Genetic --- Genetics --- Investigative Technics --- Investigative Technic --- Investigative Technique --- Technic, Investigative --- Technics, Investigative --- Technique, Investigative --- Techniques, Investigative --- Methodological Studies --- Methodological Study --- Procedures --- Studies, Methodological --- Study, Methodological --- Method --- Procedure --- Analysis, DNA Sequence --- DNA Sequence Determination --- DNA Sequence Determinations --- DNA Sequencing --- Determination, DNA Sequence --- Determinations, DNA Sequence --- Sequence Determinations, DNA --- DNA Sequence Analysis --- Sequence Determination, DNA --- Analyses, DNA Sequence --- DNA Sequence Analyses --- Sequence Analyses, DNA --- Sequencing, DNA --- Analysis, Nucleic acid sequence --- Analysis, Nucleotide sequence --- Base sequence (Nucleic acids) --- DNA sequence --- Nucleic acid sequence analysis --- Nucleotide sequence analysis --- RNA sequence --- Sequence, Nucleotide --- Bio-informatics --- Biological informatics --- methods. --- Information science --- Computational biology --- Systems biology --- Nucleic acids --- Nucleotides --- Sequence alignment (Bioinformatics) --- Data processing --- Analysis --- Bioinformatics. --- Human genetics. --- Human Genetics. --- Heredity, Human --- Human biology --- Physical anthropology