Maestro from Schrodinger can display both the predicted secondary structure elements (SSE) of the target and the SSE of the templates above the alignment dynamically (namely if you change the alignment the SSEs are changed accordingly).
Alternatively you can use the following commercial free tools:
ESPript (http://espript.ibcp.fr/ESPript/ESPript/): can create an image of your alignment with the SSEs of your templates above it. No SSE of the target is displayed though.
MolIDE (http://dunbrack.fccc.edu/molide/index.php): I have the notion that this alignment editor (and not only) can display both the predicted SSE of the target and the SSE of the templates. However, I didn't manage to run it yet due to compilation problems. I intend to give it a try in the near future.
STRAP (http://3d-alignment.eu/): it can do both but the GUI is not handy in Linux (windows and fonts are unequal, etc.).
Finally you can add a row with the secondary structure (as you wrote it in your email) above each sequence in your alignment editor. I prefer Jalview and like to play around with groups and colors. See the attached image for an example. SSE of your templates can be retrieved from PDB (e.g. http://www.pdb.org/pdb/explore/sequenceText.do?structureId=2IXF&chainId=A) whereas the SSE of your target can be predicted by Jpred3 (http://www.compbio.dundee.ac.uk/www-jpred/).
Suppose i have two templates, and a target sequence. Instead of sequence alignment based file, i want to consider the secondary structure information, like given below
H=Helix, C=Coil, S-Strand, I=Indels
Is it possible to get the alignment in this case for multiple templates against the target sequence( whose structure can also be represented as best aligned folds)
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