I needed to predict the secondary structure of amino acid sequences, already in a multiple sequence alignment (MSA). This means that the sequences had gaps, which could be a problem. I searched the net for a suitable, easy-to-use application or online server.
Somehow, none of the tools I found seemed to be suitable for me. I needed a program that can load the MSA (no need to generate it by itself), predict the secondary structure for each sequence independently (not making a consensus secondary structure prediction) and graphically present the result over the sequences (as they are aligned, including gaps).
Turns out, I have had the answer all the time: UCSF Chimera. I have mentioned this powerful program before. It can open a protein MSA (let’s say in FASTA format) in it’s own window. You simply go to Structure > Secondary Structure > Show predicted. That’s it! You can customise the appearance by Info > Region Browser.
After, it is very easy to export the result as EPS and later open it with Inkscape, if some polishing of the image is needed.