Practice on Orthology prediction
1) Copy and paste the following sequence into the most appropriate NCBI Blast search.
MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGP DEAPRMPEAAPPVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAK SVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHE RCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNS SCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKKGEPHHELP PGSTKRALPNNTSSSPQPKKKPLDGEYFTLQIRGRERFEMFRELNEALELKDAQAGKEPG GSRAHSSHLKSKKGQSTSRHKKLMFKTEGPDSD
2) Explore the score, identity, e-value, and alignment of the best-scoring hit. What is the probable source (species) for this sequence?, why do you get so many similar hits in the same species?
3) Repeat the search using as a limit the species name of Drosophila melanogaster [in Choose Search set, Organism]. Compare the relevant values and the alignment with the result above.
4) Get the best hit in Drosophila obtained above and use it for a reverse Blast against the human sequence. Is this a Best bidirectional hit (BBH) of our human protein? what would you conclude about their orthology or paralogy relationships.
5) Now we will explore the orthology relationships of human TP53 in Mouse, Chicken, Ciona intestinalia and Drosophila in several on-line databases. You can search TP53 by name or by Blast searchers in the different databases. To help you compare results you can fill in a table like this one:
Database | Type of relationship (one-to-one, etc) | Human | Mouse | Ciona intestinalis | Drosophila melanogaster
Let us try the following databases, explore the different structures and type of information that they provide:
In-paranoid An extension of BBH tto include in-paralogs
Egg NOG A clustering method to derive orthologous groups
Ensembl A clustering + phylogeny-based method
PhylomeDB A phylogeny-based, gene-centric method
6) If you have time left, have a look at the “Quest for Orthologs” initiative and explore other databases of the many available