Week One:

Overview of IMG-ACT   source file

The goal of this annotation project is for students to arrive at evidence-based conclusions about gene structure and function using web-based sequence searches.

Week Two:

Pathway assignments  source file

Basic information module  source file

Learning goals:  Compare gene sequences between different organisms.  Navigate genome database (img/edu) and online lab notebook.  Acquire sequence data for subsequent searches.

Week Three:

Sequence-based similarity and HGT modules  source file

Learning goals:  Conduct homology searches.  Deduce gene product structure and function from sequence data.  Investigate sequence composition of gene in comparison to genome.  Explore evolutionary implications of gene context.

Week Four:

Alternative start codons and novel ORFs module  source file

Learning goals:  Construct a gene model.  Discover new genes.

Week Five:

Cellular localization module  source file

Learning goals:  Detect transmembrane domains and signal peptides.  Predict location of protein product based on probability data.  Evaluate whether or not prediction is consistent with function.

Week Six:

Structure-based functional analysis module  source file

Learning goals:  Analyze structural predictions based on probability data associated with consensus sequences for functional domains (HMMs).

Week Seven:

Enzymatic function module  source file

Learning goals:  Identify cellular pathways and structures in which gene may function.  Classify gene based on homology to enzymes.

Week Eight:

Paralogs and pseudogenes  source file

Learning goals:  Compare homologous gene products within the same genome (paralogs).  Distinguish between orthologs and paralogs.  Evaluate structural requirements of a pseudogene.

Week Nine:

Multiple sequence alignments and phylogenetic trees modules  source file

Learning goals:  Compare homologous gene products from different genomes (orthologs).  Identify conserved regions and correlate to structural data (i.e., secondary structure, functional domains, active site, TMH).  Construct evolutionary history of genes and compare to organismal phylogeny.

Week Ten:

IMG-ACT Lab Reports  source file

Transfer results from online notebook to lab report, a format compatible for IMG database.  Propose an annotation for assigned gene based on analysis of data from all modules.

 

— last updated 02 June 2010 —