I have a few hundred PDB files. I have extracted the sequences in FASTA format and performed a multiple sequence alignment. On the other hand, I have assigned the secondary structure using STRIDE.
Now I would like to visualise the alignments annotated with the secondary structure for each sequence.
So firstly I would like to know which protein sequence alignment formats can contain secondary structure annotations and secondly I would like to know of viewers that are able to parse those formats and to display the multiple sequence alignment with secondary structure information for each sequence.
OK, after doing some research, it seems that the Stockholm (Pfam) format could be a straightforward option. For the visualisation Belvu should work, in theory. But I have not checked yet.
If you align the sequences using PROMALS 3D (http://prodata.swmed.edu/promals3d/promals3d.php), the output will display the alignment in Clustal format (this can be reformatted with programs like for instance Jalview) and the secondary structure will be distinguished in colours. The alignment will be performed according to the structure similarity and not solely according the sequence homology which is superior to the common algorithms used for sequences of unknown structure.
Thanks Vladimir. Your answer implies that the Clustal format support secondary structure mark-up. Is that correct? I cannot find any documentation on the subject.
As far as I know, Jalview cannot read secondary structure information directly from a file (at least not a Stockholm-formated file). What it can do is importing that information from secondary structure prediction servers.
Yes, PROMALS 3D is indeed great software, but we have developed our own structure-based sequence alignment method, MUSA-REFLEXSA, that we are currently testing prior to publication. That is why I am interested in a MSA format that supports SS mark-up and in a viewer that can understand that format and display the SS directly from the file.
PROMALS colours the secondary structure in the Clustal format alignment. Perhaps you could ask the author (Nick Grishin) how he dos that.
After testing different alternatives, finally the combination of the Stockholm (Pfam) format and the Pfaat viewer happens to be fair enough for our purposes.
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