Jalview 2.9

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New Features

General

  • Linked visualisation and analysis of DNA and Protein alignments:
    • Translated cDNA alignments shown as split protein and DNA alignment views
    • Codon consensus annotation for linked protein and cDNA alignment views
    • Link cDNA or Protein product sequences by loading them onto Protein or cDNA alignments
    • Reconstruct linked cDNA alignment from aligned protein sequences
  • Jmol integration updated to Jmol v14.2.14
  • Import and export of Jalview alignment views as BioJSON
  • New alignment annotation file statements for reference sequences and marking hidden columns
  • Reference sequence based alignment shading to highlight variation
  • Select or hide columns according to alignment annotation
  • Find option for locating sequences by description
  • Conserved physicochemical properties shown in amino acid conservation row
  • Alignments can be sorted by number of RNA helices

Application

  • New cDNA/Protein analysis capabilities
    • Get Cross-References should open a Split Frame view with cDNA/Protein
    • Detect when nucleotide sequences and protein sequences are placed in the same alignment
    • Split cDNA/Protein views are saved in Jalview projects
  • Use REST API to talk to Chimera
  • Selected regions in Chimera are highlighted in linked Jalview windows
  • VARNA RNA viewer updated to v3.93
  • VARNA views are saved in Jalview Projects
  • Pseudoknots displayed as Jalview RNA annotation can be shown in VARNA
  • Make groups for selection uses marked columns as well as the active selected region
  • Calculate UPGMA and NJ trees using sequence feature similarity
  • New Export options
    • New Export Settings dialog to control hidden region export in flat file generation
    • Export alignment views for display with the BioJS MSAViewer
    • Export scrollable SVG in HTML page
    • Optional embedding of BioJSON data when exporting alignment figures to HTML
  • 3D structure retrieval and display
    • Free text and structured queries with the PDBe Search API
    • PDBe Search API based discovery and selection of PDB structures for a sequence set
  • JPred4 employed for protein secondary structure predictions
  • Hide Insertions menu option to hide unaligned columns for one or a group of sequences
  • Automatically hide insertions in alignments imported from the JPred4 web server
  • (Nearly) Native ‘Quaqua’ dialogs for browsing file system on OSX
    LGPL libraries courtesy of http://www.randelshofer.ch/quaqua/
  • changed ‘View nucleotide structure’ submenu to ‘View VARNA 2D Structure’
  • change “View protein structure” menu option to “3D Structure …”

Applet

  • New layout for applet example pages
  • New parameters to enable SplitFrame view (file2,enableSplitFrame, scaleProteinAsCdna)
  • New example demonstrating linked viewing of cDNA and Protein alignments

Development and deployment

  • Java 1.7 minimum requirement for Jalview 2.9
  • Include installation type and git revision in build properties and console log output
  • Jalview Github organisation, and new github site for storing BioJsMSA Templates
  • Jalview’s unit tests now managed with TestNG

Issues Resolved

Application

  • Escape should close any open find dialogs
  • Typo in select-by-features status report
  • Consensus RNA secondary secondary structure predictions are not highlighted in amber
  • Missing gap character in v2.7 example file means alignment appears unaligned when pad-gaps is not enabled
  • First switch to RNA Helices colouring doesn’t colour associated structure views
  • ID width preference option is greyed out when auto width checkbox not enabled
  • Stopped a warning dialog from being shown when creating user defined colours
  • ‘View Mapping’ in structure viewer shows sequence mappings for just that viewer’s sequences
  • Workaround for superposing PDB files containing multiple models in Chimera
  • Report sequence position in status bar when hovering over Jmol structure
  • Cannot output gaps as ‘.’ symbols with Selection -> output to text box
  • Flat file exports of alignments with hidden columns have incorrect sequence start/end
  • ‘Aligning’ a second chain to a Chimera structure from Jalview fails
  • Colour schemes applied to structure viewers don’t work for nucleotide
  • Loading/cut’n’pasting an empty or invalid file leads to a grey/invisible alignment window
  • Exported Jpred annotation from a sequence region imports to different position
  • Space at beginning of sequence feature tooltips shown on some platforms
  • Chimera viewer ‘View | Show Chain’ menu is not populated
  • ‘New View’ fails with a Null Pointer Exception in console if Chimera has been opened
  • Mouseover to Chimera not working
  • Miscellaneous ENA XML feature qualifiers not retrieved
  • NPE in annotation renderer after ‘Extract Scores’
  • If two structures in one Chimera window, mouseover of either sequence shows on first structure
  • ‘Show annotations’ options should not make non-positional annotations visible
  • Subsequence secondary structure annotation not shown in right place after ‘view flanking regions’
  • File Save As type unset when current file format is unknown
  • Save as ‘.jar’ option removed for saving Jalview projects
  • Colour by Sequence colouring in Chimera more responsive
  • Cannot ‘add reference annotation’ for a sequence in several views on same alignment
  • Cannot show linked products for EMBL / ENA records
  • Jalview’s tooltip wraps long texts containing no spaces

Applet

  • Jmol to JalviewLite mouseover/link not working
  • JalviewLite can’t import sequences with ID descriptions containing angle brackets

General

  • Cannot export and reimport RNA secondary structure via jalview annotation file
  • Random helix colour palette for colour by annotation with RNA secondary structure
  • Mouseover to cDNA from STOP residue in protein translation doesn’t work.
  • hints when using the select by annotation dialog box
  • Jmol alignment incorrect if PDB file has alternate CA positions
  • FontChooser message dialog appears to hang after choosing 1pt font
  • Peptide secondary structure incorrectly imported from annotation file when annotation display text includes ’e’ or ‘h’
  • Cannot set colour of new feature type whilst creating new feature
  • cDNA translation alignment should not be sequence order dependent
  • ‘Show unconserved’ doesn’t work for lower case sequences
  • Nucleotide ambiguity codes involving R not recognised

Deployment and Documentation

Application Known issues

  • Incomplete sequence extracted from PDB entry 3a6s
  • Misleading message appears after trying to delete solid column.
  • Jalview icon not shown in dock after InstallAnywhere version launches
  • Fetching EMBL reference for an RNA sequence results fails with a sequence mismatch
  • Corrupted or unreadable alignment display when scrolling alignment to right
  • ArrayIndexOutOfBoundsException thrown when remove empty columns called on alignment with ragged gapped ends
  • auto calculated alignment annotation rows do not get placed above or below non-autocalculated rows
  • Jalview dekstop becomes sluggish at full screen in ultra-high resolution
  • Cannot disable consensus calculation independently of quality and conservation
  • Mouseover highlighting between cDNA and protein can become sluggish with more than one splitframe shown

Applet Known Issues

  • Core PDB parsing code requires Jmol
  • Sequence canvas panel goes white when alignment window is being resized