Release Notes for Sequence Viewer 3.7 (March 24, 2015)

New Features and Improvements

Bug fixes

  • Fixed visualization of Primer BLAST results
  • Fixed rendering issues in flip strand mode
  • Fixed regression in PDF renderings
  • Fixed track title to correctly reflect log base scaling

Release Notes for Sequence Viewer 3.6 (March 4, 2015)

New Features and Improvements

  • Added a function to display pure peptide track, without any gene records in the same annotation
  • SNP insertions/deletions rendering improved to visually reflect the semantics
  • Better diagnostics for private data tracks access control issues
  • Search improved to better work on local (uploaded) sequences, added performance optimizations
  • Graph track names improved to reflect the scaling parameter
  • Alignment tooltips improved to better display mate pairs
  • Improved rendering of narrow features to include strand orientation arrows

Bug fixes

  • Fixed issues with configuration failures on long requests
  • Fixed label overlap issues in graphics rendering
  • Fixed internal configuration error when uploaded data key was passed via URL parameter

Release Notes for Sequence Viewer 3.5 (December 18, 2014)

New Features and Improvements

  • Support for touch interface on Windows 8 laptops and tablets
  • Improved visualization of local molecules with annotations
  • Improved performance of molecule initialization and view configuration
  • Better rendering and tooltips for indel variations
  • Improved rendering of BAM/cSRA reads for PCR duplicated and contaminated reads
  • Switched to new, more reliable URL shortening service (goo.gl) ("link to" functions)
  • Better rendering of intron features
  • Genes track – added combined rendering of V/D/J segments and C region features
  • Invalid parameter initialization now has improved error message and offers a feedback to report issues
  • Added support for SNP tracks for Phase 3 - 1000 Genomes Project
  • Updated tooltip for GRC curation issues to reflect Affects and Fix versions
  • Graph visualization now offers log2 and linear mode with recalculation
  • Improved display of protein sequences: only showing residues different from the predicted sequence, reduce visual clutter
  • Ability to read more formats introdusced to user uploaded data functionality

Bug fixes

  • Configure dialog – fixed Load Default hanging on views with BLAST alignments
  • Fixed incorrect codon visualization across the splice junction
  • Fixed broken parameter Orfthreshold for Six Frame Translation track
  • Fixed search by protein accessions
  • Fixed feature selection of long features in full screen mode
  • Fixed Grayscale mode for ClinVar track tooltips
  • Fixed incorrect Marker rendering, making it exactly 1-bp wide

Release Notes for Sequence Viewer 3.4 (September 22, 2014)


New Features and Improvements

  • Visualization of Graphs – added new options to better display high dynamic range graphs by showing them in Logarithmic scale or in Linear Scale while Clipping Outliers based on standard deviation
  • Improved visualization of Sequence Track and other text by using improved fonts
  • Removed 'Display Options' from Configuration Dialog. Added 'Preferences' option to the Tools menu where display parameters can be set.
  • Track tooltips have been changed to offer a more compact view
  • Configuration Dialog – added methods to select/deselect multiple tracks using Ctrl/Shift + mouse click
  • Improved display of features annotated deep on components/scaffolds (like  KI635571.1) http://www.ncbi.nlm.nih.gov/projects/sviewer/?id=KI635571.1
  • Added support for the NCBI authentication protocol for restricted datasets
  • Improved internal per track error processing to better report inaccessible tracks
  • Improved upload of large files (user upload data)
  • Improved some cryptic error messages
  • Improved color schemas for users with color vision deficiency

Bug fixes

  • Fixed mouse selection of tracks in Configuration Dialog
  • Fixed issue with Link to View, truncates the title
  • Fixed image loading errors in MS IE browser

Release Notes for Sequence Viewer 3.3 (June 23, 2014)


New Features and Improvements

  • Performance optimizations in graphics rendering backend
  • Implemented new FASTA downloads for mRNA, Proteins and Exons
  • Improved tooltips renderings, to better separate different sections
  • Implemented track search using search toolbar panel and Configuration dialog
  • Improved search for sequences

Bug fixes

  • Fixed issue with user uploaded tracks order and it sometimes not turned on automatically
  • Fixed issues with track display/registration on BLAST pages
  • Fixed issue with PrimerBLAST track disappears if user tries to upload some custom data
  • Fixed Flat File download bug, not showing features on the negative strand
  • Fixed issues with [x] Hide track function
  • Fixed horizontal scrolling does not always work when mouse dragging the low part of the image
  • Fixed tooltip processing error for GWAS track
  • Improved statistics collection for external embedders
  • Fixed unwanted horizontal scroll bar in Marker Position dialog
  • Fixed unwanted spaces in Selected Range tooltip (SNP pages)

Release Notes for Sequence Viewer 3.2 (April 23, 2014)


New Features and Improvements

  • Data Upload interface now supports multi-track upload See documentation
  • Improved display of long track titles
  • New GUI control and embedding API parameter to control display of track titles. "No track title" mode allows more compressed display with more data to display and analyze.
  • Configuration dialog for graph tracks now supports customizable display style parameters
  • Improved tooltips for variation features to better reflect clinical significance
  • Improved SV embedding documentation
  • Implemented initial support for touch screen user interface (swipe)
  • Implemented new parameter (Histogram threshold) to toggle between variation histogram and showing actual features

Bug fixes

  • Fixed some issues with data upload on MS IE 11
  • Fixed bug with feature context sub-menu "Views & Tools"
  • Fixed various integration issues with BLAST and Primer BLAST
  • Fixed bug with grayscale color mode for Clinical Channel track
  • Fixed issues with ruler bar navigation with simultaneously open Sequence Text window
  • Fixed marker position error (1-base less) in Sequence Text
  • Fixed tooltip defect when spanning icon appears over text
  • Fixed tooltip label renderings for features with large number of qualifiers

Release Notes for Sequence Viewer 3.1 (January 27, 2014)


New Features and Improvements

  • Improved compatibility with Internet Explorer for users embedding Sequence Viewer on their WEB sites (cross-domain embedding)
  • Improved performance and response time

Bug fixes

  • Fixed issues with BLAST and PrimerBLAST compatibility
  • Fixed server-side issues causing periodic outages
  • Fixed bugs with sometimes incorrect protein translations in the graphical display under CDS
  • Fixed numerous issues with user data upload and track registration
  • Fixed rendering issues (text override) in tooltips
  • Fixed bug with showing same tooltips for different features in the same coordinates (GRC issues)

Release Notes for Sequence Viewer 3.0 (November 14, 2013)


New Features and Improvements

  • Implemented new service for uploading user tracks
  • Track upload configuration integrated with MyNCBI account, uploads for authorized are remembered longer
  • Greatly improved set of readers for user data formats (GFF, VCF, BED)
  • Improved Sequence Viewer embedding for external WEB sites, CGI calls are now made directly to NCBI, without need to program proxy-redirection on the customers web site
  • Improved file download to create context specific filenames

Bug fixes

  • Fixed bug with certain tooltips not opening on “Genes” track
  • Updated legend documentation to better reflect heat-map rendering styles for graphs
  • Fixed bug with URL 404 error for PDF downloads
  • Fixed bug with uploading NCBI Genome Workbench project files
  • Fixed issues with displaying Parent-Child relationships from GFF annotation file
  • Fixed issues with showing multiple markers (bookmarks) in PDF
  • Fixed bug with displaying protein (coding error) in text view

Release Notes for Sequence Viewer 2.27 (August 12, 2013)


New Features

  • Data upload service now implements track discovery mode
  • New tracks implemented for Contigs and Tiling Path
  • Implemented interface to VDB cSRA graphs storage (at NCBI)
  • Order of tracks on the screen can be changed with drag and drop. Tracks can now be closed by [x] button
  • New help web site based on content management system (CMS)
  • Implemented heat map graph visualization

Bug fixes and Improvements

  • Fixed bug with marker disappearance after updating a view
  • Internal infrastructure update to better isolate production testing/development data
  • Viewer initialization improved to better handle possible delays on complex visualization case or slow network
  • Fixed various issues with PDF rendering, improved compatibility with PDF editors (like Adobe Illustrator)
  • Improved standards conformance making HTTP links with spaces (spaces should be masked)
  • Improved performance of tooltips
  • GRC Issue features are now linked (tooltips) back to GRC issue report
  • Toolbar edit box (Search) – enabled local menu to allow cut and paste functionality

Last updated: 2015-03-25T16:29:53-04:00