ورود به حساب

نام کاربری گذرواژه

گذرواژه را فراموش کردید؟ کلیک کنید

حساب کاربری ندارید؟ ساخت حساب

ساخت حساب کاربری

نام نام کاربری ایمیل شماره موبایل گذرواژه

برای ارتباط با ما می توانید از طریق شماره موبایل زیر از طریق تماس و پیامک با ما در ارتباط باشید


09117307688
09117179751

در صورت عدم پاسخ گویی از طریق پیامک با پشتیبان در ارتباط باشید

دسترسی نامحدود

برای کاربرانی که ثبت نام کرده اند

ضمانت بازگشت وجه

درصورت عدم همخوانی توضیحات با کتاب

پشتیبانی

از ساعت 7 صبح تا 10 شب

دانلود کتاب Introduction to Bioinformatics in Microbiology (Learning Materials in Biosciences)

دانلود کتاب مقدمه ای بر بیوانفورماتیک در میکروبیولوژی (مواد آموزشی در علوم زیستی)

Introduction to Bioinformatics in Microbiology (Learning Materials in Biosciences)

مشخصات کتاب

Introduction to Bioinformatics in Microbiology (Learning Materials in Biosciences)

ویرایش: [2 ed.] 
نویسندگان:   
سری:  
ISBN (شابک) : 3031452925, 9783031452925 
ناشر: Springer 
سال نشر: 2023 
تعداد صفحات: 262
[257] 
زبان: English 
فرمت فایل : PDF (درصورت درخواست کاربر به PDF، EPUB یا AZW3 تبدیل می شود) 
حجم فایل: 14 Mb 

قیمت کتاب (تومان) : 52,000



ثبت امتیاز به این کتاب

میانگین امتیاز به این کتاب :
       تعداد امتیاز دهندگان : 7


در صورت تبدیل فایل کتاب Introduction to Bioinformatics in Microbiology (Learning Materials in Biosciences) به فرمت های PDF، EPUB، AZW3، MOBI و یا DJVU می توانید به پشتیبان اطلاع دهید تا فایل مورد نظر را تبدیل نمایند.

توجه داشته باشید کتاب مقدمه ای بر بیوانفورماتیک در میکروبیولوژی (مواد آموزشی در علوم زیستی) نسخه زبان اصلی می باشد و کتاب ترجمه شده به فارسی نمی باشد. وبسایت اینترنشنال لایبرری ارائه دهنده کتاب های زبان اصلی می باشد و هیچ گونه کتاب ترجمه شده یا نوشته شده به فارسی را ارائه نمی دهد.


توضیحاتی در مورد کتاب مقدمه ای بر بیوانفورماتیک در میکروبیولوژی (مواد آموزشی در علوم زیستی)




توضیحاتی درمورد کتاب به خارجی

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.



فهرست مطالب

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
	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
			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
		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
		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
			4.1.2.1	 Amino Acid Substitution Matrices
			4.1.2.2	 Nucleotide Substitution Matrices
		4.1.3	 Gaps
		4.1.4	 Dynamic Programming
			4.1.4.1	 Needleman and Wunsch
			4.1.4.2	 Smith and Waterman
	4.2	 Multiple Alignment
		4.2.1	 Clustal
		4.2.2	 Other Multiple Alignment Programs
	4.3	 BLAST
		4.3.1	 NCBI BLAST
		4.3.2	 Ortholog Detection
		4.3.3	 BLAST2 sequences
		4.3.4	 Statistics
		4.3.5	 Variants of BLAST
	4.4	 Activities
		4.4.1	 Pairwise Alignment
		4.4.2	 Multiple Alignment with ClustalX
		4.4.3	 BLAST
	References
5: Primer Design
	5.1	 Background for Oligonucleotide Design
		5.1.1	 Practical Approach to Oligonucleotide Design Whether of Exploratory Nature or for Diagnostic Purpose
			5.1.1.1	 Exploratory Applications
			5.1.1.2	 Diagnostics Applications
	5.2	 General Rules for Design of Oligonucleotides
		5.2.1	 Lengths of PCR Primers and Products
		5.2.2	 Lengths of Oligonucleotide Hybridization Probes
	5.3	 Sequence Comparison
		5.3.1	 String Comparison by Score
		5.3.2	 Nearest Neighbor Comparisons of Duplex Stability
		5.3.3	 Design of Primers for PCR and “Kwok’s Rules”
		5.3.4	 Design of Probes for Hybridization
	5.4	 Tm Calculations
		5.4.1	 Estimation of Tm by Formula
		5.4.2	 Formamide Considerations
		5.4.3	 Estimation of Tm by Nearest Neighbor Prediction
	5.5	 Special Applications
		5.5.1	 Exploratory Applications
			5.5.1.1	 Degenerate Primers and Probes
			5.5.1.2	 Nested PCRs
		5.5.2	 Diagnostic Applications
			5.5.2.1	 Primers for Multiplex PCR
			5.5.2.2	 SNP Analysis
	5.6	 Data Formats
	5.7	 Programs
	5.8	 Activities
		5.8.1	 Exploratory Primers with Primer3 for Recognition of Single DNA Sequences
		5.8.2	 Diagnostic Primers with PrimerBLAST
	Further Reading
		Introduction to practical work with PCR as well to the historical background is found in Sambrook and Russell (2001):
		References
6: Introduction to Phylogenetic Analysis of Molecular Sequence Data
	6.1	 Background
	6.2	 Understanding the Phylogenetic Tree
	6.3	 Assumptions About Data in Order to Perform Phylogenetic Analysis
	6.4	 Phylogenetic Model Parameters
		6.4.1	 The Tree Structure
		6.4.2	 Substitution Matrix and Evolutionary Models
		6.4.3	 Weighting of Characters
	6.5	 Phylogenetic Methods
		6.5.1	 Maximum Parsimony
		6.5.2	 Distance Matrix/Neighbor Joining
		6.5.3	 Maximum Likelihood
		6.5.4	 Bayesian (Mr. Bayes) Inference of Phylogeny
	6.6	 Comparison of Phylogenetic Methods
		6.6.1	 Bootstrap
	6.7	 Whole Genome Phylogeny
		6.7.1	 Core Phylogeny
		6.7.2	 Genome Distance Phylogeny
	6.8	 Data Formats
	6.9	 Phylogenetic Program Packages
	6.10	 Activities
		6.10.1	 Neighbor Joining Phylogeny
	Further Reading
		References
7: Sequence-Based Classification and Identification
	7.1	 Introduction
	7.2	 Classification of Prokaryotes
		7.2.1	 Classification Based on 16S rRNA Gene Sequence Comparison
		7.2.2	 From DNA–DNA Hybridization of Total DNA to WGS for Classification
			7.2.2.1	 ANI
			7.2.2.2	 GGDC
		7.2.3	 Classification Based on Core Genome Analysis and Multilocus Sequence Analysis (MLSA)
	7.3	 Classification of the Taxonomic Hierarchy
		7.3.1	 Classification of Species
		7.3.2	 Classification of Genera
		7.3.3	 Classification of Families, Orders, Classes, and Phyla
	7.4	 Rules for the Naming of a New Prokaryote
		7.4.1	 Bacterial Species Names Are Linked to the Type Strain
			7.4.1.1	 Example of an Old Bacterial Name that Never Changed
			7.4.1.2	 Example of Taxon with Many Reclassifications and Changes in Genus Name
	7.5	 The Benefits of Sequence-Based Identification
		7.5.1	 16S rRNA Sequence-Based Identification, Step-by-Step
		7.5.2	 16S rRNA-Based Identification Without Culture
		7.5.3	 Sequence-Based Identification of Fungi
		7.5.4	 Sequence-Based Identification of Protists
	7.6	 Strain Identification by WGS Analysis
		7.6.1	 SNP
		7.6.2	 OGRI for Strain Level Conformation and Identification
		7.6.3	 OGRI for Fungi
		7.6.4	 Identification of E. coli K12
	7.7	 Activity
		7.7.1	 16S rRNA Gene Sequence-Based Identification
	References
8: 16S rRNA Amplicon Sequencing
	8.1	 Use of 16S rRNA Amplicon Sequencing, Generation of Data, and Bioinformatics Pipelines
		8.1.1	 Use of 16S rRNA Amplicon Sequencing and Generation of Raw Data
		8.1.2	 Bioinformatical Pipelines to Analyze Data
	8.2	 Data Analysis
		8.2.1	 Quality Trim by Sequence
		8.2.2	 Pairing of Reads
	8.3	 Removal of Chimeras and DNA from Other Domains or Life
	8.4	 Grouping of Reads into OTUs
	8.5	 Alignment of OTUs and Association of OTUs with Taxonomic Units
	8.6	 α-(Within Group) and β-Diversity (Between Groups) Comparison
		8.6.1	 Rarefaction Analysis
	8.7	 Taxonomic Comparisons
		8.7.1	 Generation and Interpretation of Heatmaps and Boxplots
	8.8	 Principal Coordinates Analysis (PCoA)
	8.9	 Prediction of Function
	8.10	 Activity QIIME2
		8.10.1	 Installation
		8.10.2	 Running QIIME2
		8.10.3	 Download Data
		8.10.4	 Change Data Format to QIIME2 Artifacts
		8.10.5	 Demultiplexing Sequences
		8.10.6	 Denoising
		8.10.7	 Visualization Summaries of the Data
		8.10.8	 Phylogenetic Tree
		8.10.9	 α- and β-Diversity Analyses
		8.10.10 Alpha Rarefaction Plotting
		8.10.11 Taxonomic Analysis
		8.10.12 Exporting Data
		8.10.13 Filtering Data
		8.10.14 Good to Know When Working with QIIME2
			8.10.14.1 Already Demultiplexed Data
			8.10.14.2 Merging of Paired-End Reads
			8.10.14.3 Train Your Classifier
			8.10.14.4 Plugins
			8.10.14.5 Decontamination
	References
9: Full Shotgun DNA Metagenomics
	9.1	 Background
	9.2	 Sequencing Strategies and Data Types
	9.3	 Analysis of Full DNA Shotgun Sequence Data
	9.4	 MG-RAST
	9.5	 Upload and Analyze on MG-RAST
	9.6	 Activities
		9.6.1	 Full DNA Metagenome–Shotgun DNA Metagenomics
	References
10: Transcriptomics
	10.1	 Introduction to Transcriptomics
	10.2	 Experimental Design
	10.3	 Preparing a RNA-seq Library
		10.3.1	 Step 1: Isolation of RNA
		10.3.2	 Step 2: Depletion or Removal of rRNA
		10.3.3	 Step 3: Convertion of RNA into Complementary DNA (cDNA)
		10.3.4	 Step 4: Addition of Sequencing Adaptors
		10.3.5	 Step 5: PCR Amplification (Enrichment)
		10.3.6	 Step 6: Quality Control of the Library
	10.4	 Sequencing
	10.5	 Data Management (Sequence Reads)
		10.5.1	 Raw Data
		10.5.2	 Alignments of Sequence Reads
		10.5.3	 Normalization of Data
	10.6	 Differential Gene Expression
	10.7	 Conclusion
	References
11: Sequenced-Based Typing and Prediction of Function
	11.1	 Background of Prokaryotic Populations and Population Genetics
		11.1.1	 Mutation
		11.1.2	 Selection
		11.1.3	 Genetic Drift
		11.1.4	 Migration
		11.1.5	 The Biological Consequences of Population Genetics of Prokaryotes
	11.2	 Multilocus Sequence Typing (MLST)
		11.2.1	 MLST
		11.2.2	 Multilocus Sequence Analysis
	11.3	 Whole Genome-Based Typing
		11.3.1	 Whole Genomic Multilocus Sequence Typing (wgMLST)
		11.3.2	 Single Nucleotide Polymorphisms (SNP)
		11.3.3	 Typing of Virulence, Antibiotic Resistance, and Serotype Based on the Whole Genomic Sequence
			11.3.3.1	 Prediction of Virulence Genes
			11.3.3.2	 Prediction of Antibiotic Resistance
			11.3.3.3	 Secondary Metabolites
			11.3.3.4	 Prophages
			11.3.3.5	 Plasmids Mobile Genetic Elements
			11.3.3.6	 Restriction and Modification of DNA
			11.3.3.7	 CRISPR
	11.4	 Organisms Specific Platforms for Whole Genome Sequence-Based Typing
	11.5	 Association of Genetic Trains with Metadata and Phylogeny
	11.6	 Activities
		11.6.1	 MLST Typing of Pasteurella multocida
		11.6.2	 Graphics
	Further Reading
		References
Appendix
	Abbreviation of Amino Acids
	Ambiguity Table Symbols
	Codon Tables
Index




نظرات کاربران