Hi,

I'm wondering why you use so many different files for a single project. I'm mainly doing some alignment task and some annotating of the proteins I'm working with.

Now I have the Ugene project save file *.uprj, several *.gb files and some *.aln files. I'm always a little bit confused by these amount of files that are to connected to a single project. Why do I need a *.gb file for every protein in my Ugene project? Can I declare a central *.gb file for all my annotations?

Why not using a directory as "save file" (like ccpnmr [1] does) or better a gzipped file where all these files are saved within.

[1] http://www.ccpn.ac.uk/ccpn/software/ccpnmr-analysis

Well, yes, sometimes the central .gb file can be a good solution, so we will add this feature to our TODO-list. I think that we will implement it somewhere in  1.6.x.

Thanks for your suggestion!

Would it not be more convenient to have data stored in a database instead of many separate files?

Actually, this feature is planned for future release! Stay tuned for updates :)