Developed by Yu He (TA for Bio 4342), this PowerPoint presentation provides a basic overview of the common algorithms used to generate multiple sequence alignments. The presentation also illustrates how one could use Clustal Omega to generate a multiple sequence alignment for a set of orthologous proteins in order to identify conserved domains within the protein.
This walkthrough illustrates how GBrowse and the RNA-Seq tools at FlyBase can be used to identify genes with similar expression patterns. This walkthrough provides an introduction to the TopoView RNA-Seq track in FlyBase GBrowse, the FlyBase Expression Profile Search tool, and the Expression Similarity Search tool. It also illustrates how the Gene2Function web site can be used to infer the function of a D. melanogaster gene based on the functions of its orthologs in other model organisms.
This lecture from Dr. Barak Cohen discusses the major factors to consider (e.g., species to analyze, model for conserved sequences) when using phylogenetic footprinting to identify conserved regions across multiple species. The lecture also illustrates how the weight matrix model can be used to describe sequence motifs, and it provides an introduction to Magma, which uses the multiple species with multiple genes approach to discover conserved motifs.
This lecture from Dr. Jeremy Buhler discusses the limitations of the Smith-Waterman local alignment algorithm and the heuristics used by the BLAST program in order to reduce the search space and to quickly produce high-scoring local alignments.
Developed by Dr. Anton E. Weisstein (Truman State University) and Mingchao Xie (TA for Bio 4342), this lecture and exercise introduce students to the core algorithm (dynamic programming) used by many sequence alignment tools (e.g., BLAST). The exercise includes a spreadsheet with a dynamic programming matrix that allows students to explore the impact of different types of alignments (i.e. global, semiglobal, and local) and scoring systems on the resulting sequence alignment.
