Uploaded image for project: 'Jalview'
  1. Jalview
  2. JAL-732

automatically associate PDB files dragged onto an alignment with sequences that have high similarity and matching IDs

    XMLWordPrintable

    Details

    • Type: New Feature
    • Status: Resolved
    • Priority: Major
    • Resolution: Incomplete
    • Affects Version/s: None
    • Fix Version/s: 2.7, 2.8
    • Component/s: None
    • Labels:
      None

      Description

      many users needing sequence/structure alignment visualisation will have a number of specially prepared PDB files, and one or more alignments involving those files. It is extremely cumbersome to manually add associations between specific files and sequences in the alignment. One way this mapping could be automated is to allow the user to drag a set of files (or a directory) onto Jalview, and for each PDB file identified:
      a. Search the alignment to detect sequences with similar IDs.
      b. test similarity between PDB sequence and similarly named sequences to find those that are properly contained/contain the PDB sequence.
      c. add associations for strong matches identified in b, and optionally ask the user if they want to add in any of the other files not associated with any sequences.

        Attachments

          Issue Links

            Activity

              People

              Assignee:
              jprocter Jim Procter
              Reporter:
              jprocter Jim Procter
              Votes:
              0 Vote for this issue
              Watchers:
              0 Start watching this issue

                Dates

                Created:
                Updated:
                Resolved: