Upon successful completion of this course the student will:
-know fundamental principles and approaches in the emerging field
of marine microbial genomics and apply these to
their own research
-be able to genomic analyses to address biogeochemical and
ecological questions
-know the annotation and analysis of genome sequences of marine
bacteria and genomic analysis methods, ecological applications of
genomics, comparative genomics of marine microbes, and bioinformatics
-be able to incorporate bioinformatics approaches in their own
research, be comfortable mining the growing database of marine
microbial genomic sequences from both cultured and uncultured
organisms for specific genes and proteins, and address
large-scale questions in marine biogeochemical cycling using
genomic tools and approaches

Week 1  Bacterioplankton biology; course web page/utilities;
available marine genomes; www problem set; project suggestions/ideas

Week 2  Alignment methods; BLAST problem set; choose annotation
project (single organism or comparative)

Week 3  Sequencing methods' ORF identification; develop
annotation project outline; ORF finding problem set

Week 4  Protein databases; HMMs; COGs; FAMs; protein database
problem set

Week 5  TIGR Manatee/ONRL Automated Annotation; gene annotation
problem set

Week 6  Initial annotation project presentation/discussion/critique

Week 7  Comparative genomics, TIGR CMR; comparative genomics
problem set

Week 8  Gene trees; orthologs and paralogs; tree-building
programs; tree-building problem set

Week 9  Applications for marine genomics; functional gene discovery

Week 10  Applications for marine genomics continued; functional
gene problem set

Week 11  Ecological genomics (BAC end libraries; metagenomic
libraries); metagenomic BLAST problem set

Week 12  Proteomics

Week 13  Microarrays

Week 14  Class presentations

Week 15  Class presentations