Changes between Version 1 and Version 2 of SequenceStructureFeatures

Timestamp:

May 12, 2010, 2:58:18 PM (16 years ago)

Author:

pett

Comment:

--

SequenceStructureFeatures

@@ -13 +13 @@
     * 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
- 1. 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
+ 1. ~~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.
  1. 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
  1. When aligning in a structure sequence, consider secondary structure markups of non-structure sequences
- 1. If gaps are created while adding a sequence, make corresponding gaps in any markups
- 1. Vertical scrolling of alignment with scroll wheel
+ 1. ~~If gaps are created while adding a sequence, make corresponding gaps in any markups~~ Done.
+ 1. ~~Vertical scrolling of alignment with scroll wheel~~ Done.
  1. Show region names as tool tips
- 1. Allow add-sequence alignment parameters to be reset to defaults
- 1. Be smarter about what to use as the default gap character when adding a sequence
- 1. Aqua background -> gray, or put black border around sequence-name color swatches
+ 1. ~~Allow add-sequence alignment parameters to be reset to defaults~~ Done.
+ 1. ~~Be smarter about what to use as the default gap character when adding a sequence~~ Done.
+ 1. ~~Aqua background -> gray, or put black border around sequence-name color swatches~~ Done (gray background)
  1. "Sticky" headers (and remove Conservation/Consensus from Layout prefs)
  1. "Diffing" of sequence/node against consensus/node/remainder of alignment
  1. Symbols (cylinders, stars, etc.) in headers, and then manual header creation
  1. Extract region into new alignment
- 1. 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
+ 1. 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)
+ 1. Homology modeling through Modeller web service.
+ 1. Incorporate UniProt info into sequence display.