Investigating orphan folds with PSI-BLAST

From Master Projects
Jump to: navigation, search


About Investigating orphan folds with PSI-BLAST


Description

Background

Comparing fold usage patterns on completed genomes predicted by PSI-BLAST

A wealth of evolutionary information has become available through sequencing projects on entire genomes. Previously, this information was used to investigate protein fold evolution by predicting structural domains on a set of completed genomes. In general, such fold occurrence patterns show that older folds are more stable than youger folds.

See applet showing distribution of folds over genomes

What needs to be done

You will be looking with PSI-BLAST for protein folds that occur on just a few genomes. We will investigate any special prorties of such folds, and compare how different they are from folds with larger families.

Requirements

  • interest in protein structures, protein folds and phylogenies
  • able to read and write perl / python scripts that process PSI-BLAST output