Bioinformatics and Functional Genomics

You are responsible for one written document by the end of the course (Monday, December 21, 2009). At the midpoint of the course (Thanksgiving break), I plan to post rough drafts of everyone’s projects for discussion. Choose one of these two projects.

Project 1: analyze a genome in depth

[1] Select any genome. Let me know your choice, preferably within the first two weeks of the course.

[2] Prepare a written document in which you describe it from the five perspectives outlined in the course:
1) Catalog genomic information (genome size; number of chromosomes; GC content; isochores; number of genes; repetitive DNA; unique features)
2) Catalog comparative genomic information (ladder-and-constellation approach;
orthologs and paralogs; COGs; lateral gene transfer)
3) Mechanisms of evolution (how genome size is regulated; polyploidization; birth and death of genes; neutral theory of evolution; positive and negative selection; speciation)
4) Human disease relevance
5) Computational biology aspects (algorithms, databases, websites)

[3] Identify an outstanding research problem and how genomics approaches can be, or are being applied to solve it.

Project 2: 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. 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.