Changes between Initial Version and Version 1 of SequenceStructureFeatures


Ignore:
Timestamp:
Dec 24, 2008, 10:50:17 AM (17 years ago)
Author:
Scooter Morris
Comment:

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  • SequenceStructureFeatures

    v1 v1  
     1== Possible Future Enhancements for Chimera's Sequence/Structure Capabilities ==
     2
     3 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
     4    * (search other databases such as NR? PSI-BLAST on NR?)
     5 1. connect to our own Web service to multiple sequence alignment program (Muscle, T-Coffee, ... see [http://www.cgl.ucsf.edu/home/meng/sources.html#d 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
     6 1. allow sending template structure and template/target sequence alignment to comparative modeling program, either local or Web. ECM
     7 1. 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
     8    * on my secondary MAV to-do list. EFP
     9 1. allow editing sequence name. ECM
     10    * on my secondary MAV to-do list. EFP
     11 1. allow specifying "sequence to add" by accession code (Uniprot?). Its feature annotations would automatically come along as regions.  ECM
     12    * would we want Fetch by ID for sequences? (would we want a sequence with no structure and not aligned with any other sequences?)
     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)
     14    * on my secondary MAV to-do list. EFP
     15 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
     16 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
     17    * on my tertiary MAV to-do list. EFP
     18 1. When aligning in a structure sequence, consider secondary structure markups of non-structure sequences
     19 1. If gaps are created while adding a sequence, make corresponding gaps in any markups
     20 1. Vertical scrolling of alignment with scroll wheel
     21 1. Show region names as tool tips
     22 1. Allow add-sequence alignment parameters to be reset to defaults
     23 1. Be smarter about what to use as the default gap character when adding a sequence
     24 1. Aqua background -> gray, or put black border around sequence-name color swatches
     25 1. "Sticky" headers (and remove Conservation/Consensus from Layout prefs)
     26 1. "Diffing" of sequence/node against consensus/node/remainder of alignment
     27 1. Symbols (cylinders, stars, etc.) in headers, and then manual header creation
     28 1. Extract region into new alignment
     29 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