Bioinformatics

Bioinformatics describes the intersection of algorithms and analytical techniques used to analyze biological data. These techniques are drawn from a variety of disciplines, from computer science to statistics, and now, data science, whose focus is on the analysis of large data sets in biology.

The pages in this portion of the manual describe project ideas I have used in my classes at Chaminade University and the protocols and tools used by students to work the problems. My emphasis is on genomics. Each project is designed  to engage students in real-world bioinformatics approaches; students explore a series of project-based and inquiry-based learning activities for undergraduate biology and environmental science majors.  Phylogenetics and Systems Biology, arguably sub-disciplines of bioinformatics, are listed in their own chapters.

Current listing of topics, with links, are provided below.

• Bioinformatics I: BLAST
• Download sequences with BATCH Entrez
• Bioinformatics II: Detecting designed sequences
• Use of ORF Finder: Practice and Worked example
• Use of Virtual Ribosome: Practice and worked example
• Bioinformatics project: Evolutionary analysis of GWAS candidate genes
• GWAS and essential genes
• Identify phenotype and genotype of interest from PheGenI
• Protocol: GWAS and the PheGenI Database
• Find all SNP for your GOI
• Evaluate possible citation bias
• How to convert a distance matrix to a pairwise table with R
• Routine sequence analysis with R
• Using BLAST to predict PCR product length