Hi. Do you use stockholm format files in your work ?
If so, we (that is me, and Natasha Sherstnev) would like to hear about what kind of information you'd like to be able to write to a stockholm file. Natasha has been working on creating a new stockholm output routine for Jalview, and it would be great if we had some useful targets regarding the kinds of annotation that you really want to be encoded and any 'special' annotation needed by programs you use.
To begin with, Natasha is working on creating a stockholm writer that will generate files containing protein and RNA secondary structure annotation, and the minimal set of tags supported by PFAM and RFAM. Do let us know if you have any wishes for support beyond that !