Bioinformatics and Genomics

Lectures on sequence search, short read alignment, RNASeq, variant calling, genomic ranges, protein domains, phylogenetics, orthology, microbiome analysis and genome browsers.

Lectures

1. Basics and BLAST PDF
2. Workshop - parsing data PDF
3. Short Reads PDF
4. Genomic Data Ranges PDF
5. RNASeq PDF
6. Variation and SNPs PDF
7. Workshop: Which genes have the most SNPs? (and splice-site SNPs) PDF
8. Protein domains PDF - also see the Domains lecture slides
9. Orthology PDF
10. Workshop: Orthologs and gene networks from BLAST PDF
11. Phylogeny and Gene Families PDF
12. Sequence Evolution and Statistics PDF
13. Microbiome PDF
14. Genome Browsers PDF

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Table of contents

• Basics and BLAST
• Workshop: Parsing Data
• Short Reads
• Genomic Data Ranges
• RNASeq
• Variation and SNPs
• Workshop: SNPs per Gene and Splice Sites
• Protein Domains
• Orthology
• Workshop: Orthologs and Gene Networks
• Phylogeny and Gene Families
• Sequence Evolution and Statistics
• Microbiome
• Genome Browsers