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.