Web document 13-2. Genomics project: analyze a gene in depth

[1] Select a single protein, RNA, or DNA sequence. Unless you have a particular gene of interest, select one that is conserved across the three domains of life. Obtain a large number of homologous sequences (e.g. from a dozen to 100) in the fasta format.

[2] Perform a phylogenetic analysis. If your gene is conserved, use the sequence to make a tree of life. If it is protein-coding, analyze the substitution rate at different codon positions, describe ancestral sequences, provide evidence for neutral evolution or selection, etc.

[3] Describe specific cases in which the gene has duplicated (or been lost) across genomes. Provide evidence for duplication/deletion and date the occurrence(s).

[4] Describe conserved synteny for this gene across multiple genomes. Describe its neighboring genes.

[5] Describe regulatory regions controlling expression of this gene.