Biopython Fundamentals
Practical examples and case studies
Biopython Fundamentals
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Introduction to Biopython
What is Biopython?, Benefits and Applications of Biopython
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Installing Biopython using pip
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Biological data formats
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Sequence Manipulation and Analysis
Reading and writing Sequences
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Sequence objects and their properties
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Sequence searching and alignment
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Calculating sequence properties
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Subsetting and manipulating sequences
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Sequence Annotation and Features
Handling sequence annotations and metadata
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Extracting and modifying sequence features
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Parsing and working with GenBank files
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Visualization of sequence features
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Basic Sequence Analysis
Searching for sequence motifs using regular expressions
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Basic sequence alignment and comparison
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Calculation of sequence similarity and identity
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Finding open reading frames (ORFs)
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Advanced Sequence Analysis
Performing multiple sequence alignment (MSA)
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Sequence Motifs
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Introduction to Hidden Markov Models (HMMs)
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Phylogenetic Analysis
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Sequence motif discovery and pattern matching
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Protein structure analysis with Bio.PDB
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Working with Biological Databases
Retrieving data from NCBI databases
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Accessing and querying online biological databases
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Batch retrieval of sequences using Entrez
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Database integration and data management
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Automating Bioinformatics Workflows
Introduction to Automation in Bioinformatics
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Scripting and automating tasks with Biopython
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Writing efficient and reusable code
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Creating custom functions and modules
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Practical examples and case studies
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Biopython and NGS
Introduction to NGS data and file formats
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Quality control and filtering of NGS data
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Variant calling and analysis using Biopython
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Introduction to Biopython-compatible NGS tools
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Biopython and Genomic Data Science
Analyzing genomic data with Biopython
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Genomic data visualization using Biopython and Matplotlib
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Mining and interpreting genomic data
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Machine learning for Genomic data analysis
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Genomic Data Science workflow
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