Possible Future Enhancements for Chimera's Sequence/Structure Capabilities

1. connect to our own Web service to BLAST on PDB, provide dialog for choosing which hit structures to open, whether to show pairwise sequence alignment from BLAST (in MAV), whether to superimpose hit and query structures (with Matchmaker). Input is sequence of molecule model already open in Chimera. ECM
   • (search other databases such as NR? PSI-BLAST on NR?)
2. connect to our own Web service to multiple sequence alignment program (Muscle, T-Coffee, ... see ​list and links), show result in MAV. Input would be sequence alignment already open in Chimera, probably would have to reformat into unaligned multi-FASTA for server. ECM
3. allow sending template structure and template/target sequence alignment to comparative modeling program, either local or Web. ECM
4. given a sequence alignment and associated structure, allow showing indels on structure relative to one of the sequences in the alignment (user specifies which structure and which sequence). ECM
   • on my secondary MAV to-do list. EFP
5. allow editing sequence name. ECM
   • on my secondary MAV to-do list. EFP
6. allow specifying "sequence to add" by accession code (Uniprot?). Its feature annotations would automatically come along as regions. ECM
   • would we want Fetch by ID for sequences? (would we want a sequence with no structure and not aligned with any other sequences?)
   • perhaps allow specifying Uniprot accession or BLAST on Uniprot for existing sequences, retrieve and load feature annotations as sequence regions (would require global alignment to Uniprot sequence for correct mapping of features when the existing sequence is not identical)
   • on my secondary MAV to-do list. EFP
7. Matchmaker option to create post-fit alignment with Match->Align and refit on that to give more meaningful # of pairs and RMSD statistics along with the better alignment. Perhaps even multiple such rounds, reporting stats and showing alignment only at the end. ECM Done, though not as MatchMaker option.
8. MAV report all-by-all percent identities to Reply Log in form of a (text) matrix instead of a line for each pair. ECM
   • on my tertiary MAV to-do list. EFP
9. When aligning in a structure sequence, consider secondary structure markups of non-structure sequences
10. If gaps are created while adding a sequence, make corresponding gaps in any markups Done.
11. Vertical scrolling of alignment with scroll wheel Done.
12. Show region names as tool tips
13. Allow add-sequence alignment parameters to be reset to defaults Done.
14. Be smarter about what to use as the default gap character when adding a sequence Done.
15. Aqua background -> gray, or put black border around sequence-name color swatches Done (gray background)
16. "Sticky" headers (and remove Conservation/Consensus from Layout prefs)
17. "Diffing" of sequence/node against consensus/node/remainder of alignment
18. Symbols (cylinders, stars, etc.) in headers, and then manual header creation
19. Extract region into new alignment
20. Tree improvements: session save/restore; handle sequence addition/deletion; hide/show nodes; delete node; conservation/consensus of nodes; highlight node sequences; show numeric branch weights; restrict operations to nodes; trees where alignment isn't 1-to-1 (strikeout == done)
21. Homology modeling through Modeller web service.
22. Incorporate UniProt info into sequence display.