Introduction to bioinformatics in microbiology / Henrik Christensen, editor.
This updated and extended second edition of the textbook introduces the basic concepts of bioinformatics and enhances students' skills in the use of software and tools relevant to microbiology research. It discusses the most relevant methods for analysing data and teaches readers how to draw va...
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Full Text (via Springer) |
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| Format: | Electronic eBook |
| Language: | English |
| Published: |
Cham :
Springer,
[2023]
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| Edition: | Second edition. |
| Series: | Learning materials in biosciences.
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| Subjects: |
MARC
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| 245 | 0 | 0 | |a Introduction to bioinformatics in microbiology / |c Henrik Christensen, editor. |
| 250 | |a Second edition. | ||
| 264 | 1 | |a Cham : |b Springer, |c [2023] | |
| 264 | 4 | |c ©2023 | |
| 300 | |a 1 online resource (xvi, 246 pages) : |b illustrations (chiefly color). | ||
| 336 | |a text |b txt |2 rdacontent | ||
| 337 | |a computer |b c |2 rdamedia | ||
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| 490 | 1 | |a Learning materials in biosciences | |
| 504 | |a Includes bibliographical references and index. | ||
| 520 | |a This updated and extended second edition of the textbook introduces the basic concepts of bioinformatics and enhances students' skills in the use of software and tools relevant to microbiology research. It discusses the most relevant methods for analysing data and teaches readers how to draw valid conclusions from the observations obtained. Free software and servers available on the Internet are presented in an updated version of 2023 and more advanced stand-alone software is proposed as a second option. In addition, new tools for microbial genome analysis and new flowcharts that complement the didactic elements have been added. Exercises and training questionnaires are included at the end of each chapter to facilitate learning. The book is aimed at Ph.D. students and advanced undergraduate students in microbiology, biotechnology, and (veterinary) medicine with little or basic knowledge of bioinformatics. | ||
| 588 | 0 | |a Online resource; title from PDF title page (SpringerLink, viewed December 13, 2023). | |
| 505 | 0 | |a Intro -- Preface to Second Edition -- Contents -- List of Abbreviations -- 1: Introduction -- 1.1 Basics and History of Bioinformatics -- 1.1.1 Bioinformatics Is Integrating Many Scientific Fields -- 1.1.2 Homology -- 1.1.3 Evolution Is Related to Sequence Diversity Caused by Mutations -- 1.2 The Aim, Structure, and Outline of the Book -- 1.3 Computers and Operating Systems Required for Bioinformatics -- 1.4 Computer Programs and Pipelines -- 1.5 Activity -- Further Reading -- Basic bioinformatics text books -- References -- 2: DNA Sequence Assembly and Annotation of Genes | |
| 505 | 8 | |a 2.1 DNA Sequencing -- 2.1.1 Sanger Sequencing -- 2.1.2 Massive Parallel, Short-Read Sequencing -- 2.1.2.1 Illumina (Sequencing by Synthesis) -- 2.1.3 DNA Sequencing in Metagenomic and for Single Cell Sequencing -- 2.1.4 Real-Time, Single Molecule Sequencing -- 2.1.4.1 PacBio® -- 2.1.4.2 Nanopore Sequencing -- 2.2 DNA Sequence Assembly -- 2.2.1 Base Calling and Trimming -- 2.2.2 Assembly of DNA Sequences -- 2.2.2.1 Assembly by Overlap Consensus Methods -- 2.2.2.2 Assembly by k-mer Strategy -- 2.2.2.3 Quality Criteria of the Final Assembled DNA Sequence | |
| 505 | 8 | |a 2.2.2.4 De Novo or with Reference -- 2.3 Closing of Genomes -- 2.4 DNA Sequence Formats -- 2.5 Annotation -- 2.5.1 Elements from Comparative Genomics Aiming Annotation -- 2.6 Activities -- 2.6.1 Annotation at RAST -- Further Reading -- References -- 3: Databases and Protein Structures -- 3.1 Introduction to Bioinformatics Databases -- 3.1.1 Data Formats Used with Bioinformatics Databases -- 3.2 Organization of Databases and Bioinformatics Institutions -- 3.3 Major Bioinformatics Databases -- 3.3.1 GenBank -- 3.3.2 The European Nucleotide Archive (ENA) -- 3.3.3 Swiss-Prot and UniProt | |
| 505 | 8 | |a 3.3.4 Genomics Databases -- 3.3.5 Raw Sequence Read Datasets -- 3.3.6 Other Databases -- 3.3.7 Primary and Secondary Bioinformatics Databases -- 3.3.8 Data Formats in Bioinformatics Databases -- 3.4 Accession Numbers -- 3.5 Protein Structure Databases and Predictions -- 3.5.1 Primary and Secondary Structures -- 3.5.2 Domain Prediction and Databases -- 3.5.2.1 Single Motif -- 3.5.2.2 Multiple Motifs -- 3.5.2.3 Full Domain -- 3.5.2.4 Mixing Different Methods -- 3.5.3 Protein 3D Structure -- 3.6 Overview of Proteomics Databases and Servers -- 3.7 Help to Databases -- 3.8 Activities | |
| 505 | 8 | |a 3.8.1 Download a Sequence from NCBI -- 3.8.2 Download a Genome from NCBI -- 3.8.3 Deposition of Sequence with GenBank -- 3.8.3.1 Procedure for Single DNA Sequences -- 3.8.3.2 Genomic Sequence -- 3.8.4 Protein Structure Prediction with Swiss Model and SPDBV -- 3.9 Example Illustrating Variable Information and Redundancy of a Primary Genomic Database and Comparison to Some Other Information in the Book -- References -- 4: Pairwise Alignment, Multiple Alignment, and BLAST -- 4.1 The Pairwise Alignment Problem -- 4.1.1 Global or Local Pairwise Alignments? -- 4.1.2 Substitution Matrices | |
| 650 | 0 | |a Bioinformatics. |0 http://id.loc.gov/authorities/subjects/sh00003585 | |
| 650 | 0 | |a Microbiology |x Data processing. | |
| 700 | 1 | |a Christensen, Henrik, |e editor. |0 http://id.loc.gov/authorities/names/nb2008026602 |1 http://isni.org/isni/0000000081401463 | |
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