Phylogeny using Maximum Likelihood
Friday October 05, 2007
Practical Session |
| Aim: Build a reliable model for an unknown target sequence |
|---|
Target Sequence: MSEAAHVLITGAAGQIGYILSHWIASGELYGDRQVYLHLLDIPPAMNRLTALTMELEDCA |
Suggestions: |
| 1. Find suitable templates by performing a Blast search on the PDB |
| a. Using the Expasy system (http://www.expasy.ch/), perform a protein Blast search against the PDB b. Analyze the possible templates c. Select one (the provided tutorial files assume that you choose 1BDM) d. Visualize your template |
| 2. Align your target sequence to your template sequence |
| a. Use Jalview to perform an alignment of your target against the sequence of your template b. Create/analyze the PIR formatted alignment file suitable for modeler (already done, see file TvLDH-1bdmA.ali) |
| 3. Build 5 models for your target sequence |
| a. Analyze the python script model.py b. At the terminal prompt type: mod9v2 model.py |
| 4. Analyze your homology models |
a. Visual inspection with chimera of
|
| 5. Identify the regions that need refinement |
| a. As deduced from the visual inspection b. As deduced from ANOLEA profiles of your models |
| 6. Generate alternative ab initio conformations for the selected region using Modeller's loop routine |
| a. Analyze the python script loop.py b. At the terminal prompt type: mod9v2 loop.py |
| 7. Analyze your loop models |
| a. By visual inspection using chimera b. By re-computing ANOLEA profiles |
| 8. Submit your model to CASP |
| :-) |
Latest update 2007-12-07
