P18: Comparative Genomics. Orthologs
In this practical we will learn about orthology and paralogy relationships and how to get orthology data in ensembl-biomart.
Part I. Orthologs/Homologs/Paralogs
Phylogenetic tree
Gene Duplication
Part II. Orthology detection methods and sources
Best Reciprocal (BLAST) Hit
Synteny
Phylogenomics
Part III. Exercises
- 1) Get percentage of identity between human and mouse orthologs and between human and fruit fly orthologs of
genes involved in "Neural Development" and genes involved in "Biosynthesis".
- How many genes are there involved in each of the processes?
- What percentage of genes in each of the processes have orthologs in each of the species?
- Can you speculate on the reason why there are differences in these percentages between the two processes?
Hints: Use Biomart - Choose Ensembl 52 - to get the list of genes in each of the GO Biological Processes (you may need to search the GO-IDs in Gene Ontology .
Use Biomart - Choose homology attributes - to get % hidentity.
You may need to use unix commands.
- 2) Search for orthologs of human P53 gene in Cow, fly and Ciona intestinalis using the following methods:
- a) Best bi-directional hit approach (use NCBI Blast using limits for species.
- b) InParanoid
- c) Ensembl
- d) PhylomeDB
- What are the differences between the different methods/sites?
- If we would use reconciliation on the Gene tree available at PhylomeDB to predict orthology, would there be any pitfall? why? (use this species tree as a reference, only consider the sub-tree from the gene duplication to the P53 gene). how does phylomeDB-method address this problem?
Further Information
