If you can run a PC/Windows program, GeneDoc may be of some help.
While it will not automatically align sequences for you, it will shade
sequences with secondary structure information and allow you to
manually align the shaded sequences. Perhaps the initial alignment can
be made with the 'usual' program and then tuned for structure
considerations with GeneDoc.
Also, Structural Alignments done by the Argos Goup with the 3d_ali
effort can be downloaded viewed from the GeneDoc home page.
Hope this helps.
tnorris at molbio.uoregon.edu (Tracy B Norris) wrote:
>I am looking for a software program that will allow me to do specialized
>alignments of protein sequence. I would like to align structural elements
>of one sequence with another protein sequence. I have tried alignments in
>MegAlign, but as a consequence of alignment the program puts gaps in the
>structural elements of the first sequence (it's shorter than the other).