ObjectiveTo perform a multiple sequence alignment.

Background

Here you will become familiar with grouping sequences in the ICM Workspace and performing an alignment.

Instructions

1. Select the sequences from previous lesson (selected=highlighted blue)
2. Right click and select delete.
3. File/Open/zincFing.seq (sequence format files needs to be specified to locate the zincFing.seq file)
4. Select the sequences tab at the bottom of the ICM Workspace.
5. Click on the first sequence and then the last whilst holding the SHIFT key. All the sequence names should be highlighted in blue.
6. Right click on the selected sequences and select the Group Sequences option.
7. The grouped sequences will be displayed at the bottom of the GUI.
8. Right click on the sequence name and select Align Sequences.

Notes and things to try:

• If you have many sequences in your multiple alignment then the option to run the alignment in the background can be chosen.
• Multiple sequence alignments can also be undertaken by choosing Bioinfo/Multiple Sequence Alignment.
• Try some other sequence manipulations at this point such as searching a sequence for homology against the PDB direct from the ICM Workspace.
• The next lesson describes some of the actions you can perform using the ICM Alignment Editor.

Manual References (Web Links) Alignment Editor Align Multiple Sequences