I had few free hours during this weekend so I’ve hacked together couple of scripts that in theory could help me visualize changes between subfamilies in the protein multiple sequence alignment. In essence, I took the alignment, chose a master sequence that correspond to a known structure, removed all columns with gaps in the master sequence, and visualized fragments of the alignment (sliding window with 15 sequences) with Weblogo – software for preparing sequence logos from alignments. On the video below you can see:

• two boxes showing the same template structure (second is just rotated); size of C-alpha atoms correspond to overall conservation at that position; first few residues do not have corresponding positions in the alignment
• sequence logo of actual alignment window
• sequence logo of the whole alignment – as a reference

There are several of things I’m not yet happy with. First of all, visualization of changes on the structure is hardly readable, even with video of much higher quality (probably I should do it with Chimera’s “worm” representation). Second thing is that I have no information which species/proteins I’m looking right now at (another box with highlights on a species tree of the family?). Also, I should remove some redundancy from the alignment; sometimes sliding window contains copies of the same protein. But overall it looks promising enough to convince me to spend few more hours on this small project. However, I would probably do the final version with Processing.