Here is a list of things which may be added to SeqPup in the future, depending on your interest. Please send in your suggestions! What do you want to see to make this a good biosequence editor and analysis program?
Sequence documentation handling. Currently no provisions for documentation per sequence. This will at least change to a window for any comments and saving it into files (where file format permits). Possibly I will put effort into dealing with the features, references, etc., in a fashion along lines of Genbank/EMBL documentation structure &/or Authorin documentation. Your comments on the importance of this are desired.
Feature table parsing -- pull out subsequences from Gen/EMBL feature info.
Align, single sequence pretty print -- header, page numbering user prefs should be added.
Restriction map -- Could use some speed-up. Some would like graphic map (i.e., one line or circle w/ cut points per zyme).
Simple protein analysis routines, better protein handling.
Methods to transparently use networked child tasks (e.g., on fast compute servers).
-- DONE: see BOP use in 0.6 release
add other child apps - dna/prot distance + lsadt phylogeny analysis,
primer analysis, others ??
add user-configurable menus - read all menus from config file?
add disjoint selections to DTableView -- need for copy/paste among masks
(using table selection as clipboard for masks)
add variable color display in alignment window, as aids to aligning:
2. mask colors (e.g., stem & loop areas for RNA)
improve seq mask operations and usage
- annotate masks, choose which are used for pretty print, which for
add color picker dialog for color tables
add editable data table interface -- Done in 0.6
add name window pane resizer