I have been lucky to teach in workshops on Bioinformatics. Here are some presentations I have used in the past. Feel free to use and modify them.
Measuring microbial
Diversity
Microbes mediate many globally important processes such as carbon and nitrogen cycle. So it is important to understand how microbial communities work. The study of microbial communities include the characterization of the members of the community in terms of novelty, the structuring of the microbial community and the relationship among communities within and between ecosystems.
This presentation covers basic topics of alpha and beta diversity and analysis of microbial diversity using 16S rRNA gene sequencing.
Get the Presentation here.
Tools for microbial community analysis
This presentation covers the rationale behind multiple techniques for microbial community analysis including clone libraries , pyrosequencing, T-RFLP, DGGE, phylogenetic arrays, fingerprinting and sequencing.
Some of the techniques are outdated by next-generation sequencing though they are still inexpensive and informative to some extent.
Get the Presentation here.
Alignments and phylogenetic trees
Trees are tools to represent the evolutionary story of sequences. Alignment is the first and most critical step for comparison of sequences. In this presentation the rationale and algorithms behind alignment and phylogenetic tree reconstruction including distance- and character-based algorithms.
Get the Presentation here.
Ribosomal Databases
Ribosomal rNA gene databases are powerful tools for the study of microbial communities because they provide specialized tools as well as organized and curated data. This presentation shows the different analysis tools of the Ribosomal Database Project . One of the most popular rRNA gene Database and my favorite one (I worked there for a while).
Get the presentation here.
RDP Pyrosequencing pipeline
This presentation covers the basic processing of 16S rRNA sequences from pyrosequencing using the Ribosomal database Project.
The RDP pipeline is located here.. Image from RDP.
Get the presentation here.
BLAST
The basic local alignment search tools (BLAST) is one of the most widely used bioinformatic tools in science. In this presentattion the basic algorithm , the statistics, and the different flavors of BLAST are explained. Also is explained how to run BLAST locally and on the web.
Get the presentation here.
Functional gene repository and pipeline
This presentation covers the features of the RDP Functional gene Pipeline and repository. Here the basics of Hidden Markov models and the processing of pyrosequencing data of functional genes using the webtools are explained .
Get the presentation here.
Bioinformatic databases
This presentation covers the most commonly used bioinformatics databases
Get the presentation here.
Measuring microbial diversity
Tools for microbial community analysis
Alignments and phylogenetic trees
Ribosomal RNA databases
RDP pyrosequencing pipeline
BLAST
Functional gene repository and pipeline
Other databases