Protein MSA secondary structure

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.

It is worth mentioning that while searching for the best solution, I found some very nice tools. Among them were: PRALINE, Jpred3, APSSP2, ESPript and CFSSP.