Skip to content
Search
Close this search box.
Genomics Education Partnership logo
Contact Us
Genomics Education Partnership logo
Contact Us
Home » Lecture » Page 3

Lecture

UNIX for Consed

This PowerPoint presentation discusses the basic directory structure required by Consed and the UNIX commands used to launch Consed.

Gene Finding in Chimpanzee

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.

Generating Multiple Sequence Alignments with ClustalW

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.

Generating Multiple Sequence Alignments with Clustal Omega

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.

Overview of Multiple Sequence Alignment Algorithms

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.

Eukaryotic Comparative Genomics

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.

From Smith-Waterman to BLAST

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.

Web Databases for Drosophila

This PowerPoint presentation introduces the species-specific databases available on the web, including FlyBase and the Ensembl Drosophila melanogaster database.

Introduction to ab initio and Evidence-based Gene Finding

This PowerPoint presentation examines the use of gene prediction programs (such as Genscan) in annotation, noting some of the limitations of gene prediction programs in creating putative gene models. It also introduces the UCSC and other browsers as sources of supporting evidence.