This lecture by Dr. Sarah Elgin (Washington University in St. Louis) provides a general overview of the Genomics Education Partnership. It describes the current GEP research problem of identifying factors involved in heterochromatin formation and maintenance through comparative genomics in Drosophila.
This PowerPoint presentation provides a brief introduction to the different types of RNA-Seq evidence tracks (e.g. Bowtie, TopHat, Cufflinks) that are on the GEP UCSC Genome Browser.
This PowerPoint presentation discusses the basic directory structure required by Consed and the UNIX commands used to launch Consed.
A step-by-step tutorial that takes the student through a gene identification problem in a chimpanzee BAC sequence using predictions from a gene finder (Genscan), the UCSC Browser and BLAST.
Dr. Susan Parrish (McDaniel College) developed a basic lecture and weblem exercise (found at the end of the lecture) on using ClustalW to generate multiple sequence alignments, phylograms, and cladograms. This lecture and exercise are given prior to beginning the GEP annotation projects. Students who submit their GEP annotation projects early are then asked to generate multiple sequence alignments and phylograms of the putative proteins encoded within their assigned contig or fosmid, compared to those related proteins encoded by other Drosophila species of interest to the GEP.
Developed by Dr. Susan Parrish (McDaniel College), this PowerPoint presentation describes how Clustal Omega can be used to produce multiple sequence alignments. The multiple sequence alignments of the nucleotide sequences surrounding the transcription start sites can be used to identify core promoter motifs, while the multiple sequence alignments of protein sequences can be used to identify conserved domains. The presentation also includes a discussion of two strategies (UPGMA and Neighbor Joining) that are often used to construct phylogenetic trees.
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 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.
This primer provides an overview on how to determine the phase of donor and acceptor splice sites.
