Release Notes for Sequence Viewer 3.49 (Oct 11, 2023)

New Features and Improvements

• Modernized header and footer of full screen Sequence Viewer

Bug Fixes

• Technical updates and bug fixes

Release Notes for Sequence Viewer 3.48 (April 20, 2023)

New Features and Improvements

• You can now click a button on the right of assembly-assembly alignment tracks to open a Comparative Genome Viewer (CGV) session showing the same alignment data projected on whole genome and whole chromosome ideograms

Bug Fixes

• Fixed bugs in the track hubs configure dialog
• Additional minor tweaks and bug fixes

Release Notes for Sequence Viewer 3.47 (November 29, 2022)

New Features and Improvements

• The "hide non-coding genes" display option for gene annotation tracks now hides tRNA and rRNA genes as well
• Improved the track find in the tracks configure menu to better recognize partial search terms
• Feedback box is updated

Bug Fixes

• Fixed some bugs that affected rendering of track and feature description tooltips
• Fixed a bug in amino acid translation of 5' partial CDS features
• Additional minor bug fixes

Release Notes for Sequence Viewer 3.46 (July 19, 2022)

New Features and Improvements

• Added support for CSI index files for BAM and VCF data
• Added ability to report Ensembl identifiers, e.g. 'ENSG00000187634.11', as gene IDs

Bug Fixes

• Fixed a bug in feature rendering in SVG exported images
• Additional code updates and minor bug fixes

Release Notes for Sequence Viewer 3.45 (May 9, 2022)

New Features and Improvements

• Added ability to download VCF or BED table files from remote hosted non-tabix VCF data
• Now displaying EVA release 3 non-human variation data
• GEO and SRA tracks in the configure tracks interface are now linked to their corresponding GEO and SRA database records to make it easier to get details about these studies
• Search results in the configure tracks interface can now be sorted alphabetically
• Updated coloring scheme for ClinVar track to better accomodate variants associated with newly designated pathogenicity statuses
• Removed (x) from track name tooltips to avoid confusion over what this button does

Bug Fixes

• Fixed some coloring and rendering issues for SVG and PDF exported images
• Fixed some bugs in rendering and filtering of ClinVar track
• Fixed inconsistencies in coloring ClinVar variants with multiple pathogenicity statuses
• Additional minor tweaks and bug fixes

Release Notes for Sequence Viewer 3.44 (October 21, 2021)

New Features and Improvements

• Added ability to download VCF or BED table files corresponding to streamed tabix VCF track data, including new ability to download ClinVar and EVA RefSNP tracks
• New option to filter the display of data in the ClinVar track to show only pathogenic/likely pathogenic variants
• New ability to stream remote hosted non-tabix VCF files (up to 2000 lines)
• New 'Track Info' button on the right end of each track allows user to obtain additional information about the track and link to the Track Legend
• Marker details table now contains hyperlinks to zoom directly to marker location(s)
• Added links to GDV (Genome Data Viewer) where available from views of non-RefSeq assembly scaffolds
• Improved toolbar display on narrow mobile screens
• Supports 64-bit NCBI GI accessions

Bug Fixes

• Removed the green highlight for remote streamed tracks provided directly from Sequence Viewer; e.g. ClinVar tracks
• Fixed errors in display of translocations and inversions encoded by tabix VCF from the dbVar project
• Removed inapt track display options from feature tracks that do no have display options
• Fixed minor bugs in displaying sequence coordinates when mouse hovers over the ruler
• Fixed a bug in showing track tooltips for some SRA tracks when the display come from a shared link
• Fixed truncated toolbar display on narrow mobile screens
• Additional minor tweaks and bug fixes

Release Notes for Sequence Viewer 3.43 (July 1, 2021)

New Features and Improvements

• New functionality in the configure tracks interface to search and add aligned data tracks from the NCBI GEO, SRA, and dbGaP databases
• New ClinVar track added to the graphical view track configure menu; this track is colored by ClinVar interpretation and reports the ClinVar review status and predicted molecular consequence in the tooltips
• The sequence coordinate is reported in a hover box when the cursor is on the ruler or if the Ctrl/Cmd key is pressed
• Coloring of structural variants from remote VCF files now matches coloring for NCBI dbVar tracks
• A BLAST archive output that can be viewed in Sequence Viewer is available from the BLAST command line tool

Bug Fixes

• Fixed a bug in interpreting GFF file uploads
• Removed duplicate track options from the track configure menu
• Removed Column Quality Score and Frequency-Based Difference from the score options for alignment tracks
• Fixed a bug in displaying long features from VCF files (e.g. structural variants)
• BLAST searches initiated in Sequence Viewer now open on the newer BLAST results page
• Additional minor tweaks and bug fixes

Release Notes for Sequence Viewer 3.42 (April 8, 2021)

New Features and Improvements

• New display options for gene annotation tracks that allow the user to hide non-coding transcripts, hide gene models, show only CCDS variants, or show only RefSeq or MANE Select variants
• New display options for assembly-assembly alignment tracks that allow the user to sort aligned data by reciprocity score (e.g. first-pass versus second-pass alignments) and to hide second-pass alignments
• Now reporting the reciprocity score in the tooltips of aligned data in assembly-assembly alignment tracks
• Improved precision of heatmap rendering and better performance of streamed remote VCF data
• Improved tooltip reporting for VCF data for structural variants
• For NCBI Gene tracks showing merged transcript/CDS models, we are now reporting additional information in the tooltips, including links to FASTA and GenBank views of both the mRNA and protein records, information regarding any sequence discrepancies relative to the assembly, whether the transcript is a Select/MANE Select variant, and the matching Ensembl transcript variant if any
• A more informative label is now provided for BLAST results shown on the graphical viewer on the Primer-BLAST results view

Bug Fixes

• Corrected label reporting for intron features
• Adjusted the display setting for Primer-BLAST tracks to show all primers by default
• Fixed a bug in displaying mismatches in alignments derived from non-NCBI data
• Removed display options for some feature and alignment tracks that are not appropriate for the track data
• Fixed several security vulnerabilities
• Additional minor tweaks and bug fixes

Release Notes for Sequence Viewer 3.41 (January 28, 2021)

New Features and Improvements

• Added new display track settings for intron feature tracks, including the ability to filter by read count, sort features by read count, and sort features by strand (i.e. read direction) (documentation)
• New ability to open the view in GDV if viewing a scaffold or chromosome that is part of an assembly available in GDV (look in the menu under the accession number on the toolbar)
• Unaligned region sequences for alignment features are now highlighted in blue instead of red (can be viewed via the links in the tooltips)
• Improved "Go To" option so that the view is automatically zoomed to the sequence level of the entered coordinate or SNP ID

Bug Fixes

• Fixed a bug in detecting consensus splice sites in intron feature tracks
• Fixed a bug in setting a minimum range for graph-style track
• Corrected reporting of coordinates for small introns in NCBI Gene track downloads
• Fixed bugs in adjusting NCBI Gene track display settings when viewing tracks in GDV linked from an NCBI Gene record page
• Additional minor bug fixes

Release Notes for Sequence Viewer 3.40 (November 12, 2020)

Bug Fixes

• Improved issues with occasional track freezes when selecting or zooming to gene or SNP models
• Fixed issues preventing display of CDS annotation for some genes containing unusual translations such as ribosome slippage
• Fixed errors in reporting unaligned tails for BLAST alignments
• Removed inappropriate menu option to view NCBI Recommended Track Collections or save track sets when the molecule viewed is not an eukaryotic assembly
• Additional minor bug fixes

Release Notes for Sequence Viewer 3.39 (August 24, 2020)

New Features and Improvements

• Added information about unaligned insertions to alignment feature tooltips
• Aligned BLAST or BAM/cSRA sequence can now be downloaded from the alignment tooltip
• Updated language in gene feature tooltips
• Marker name is now reported in FASTA downloads of marker regions

Bug Fixes

• Fixed bug that prevented reporting of BLAST alignment "query" sequence in the alignment tooltips
• Fixed ability to select a sequence range within a marker region by clicking and dragging in the ruler
• Additional minor improvements and bug fixes

Release Notes for Sequence Viewer 3.38 (July 13, 2020)

New Features and Improvements

• EVA RefSNP variation tracks for non-human assemblies are now provided in the track configuration menus
• Assembly graph tracks are now found in the Comparative Genomics group
• Improved performance speed of downloads of SNP track data
• SNP data downloads containing greater than 5 million features will be exported as compressed files
• Protein features are sorted to show below the CDS annotation

Bug Fixes

• Removed duplicated tracks from the track configuration menu
• Additional minor bug fixes

Release Notes for Sequence Viewer 3.37 (May 27, 2020)

New Features and Improvements

• New ability to download NCBI SNP tracks in BED and VCF format (Documentation)
• Removed redundant download menus from right-click context menu
• Added link to download all exons to RNA feature tooltips
• Updated documentation for Accessing RNA and protein sequence data
• Virus gene annotation now shows protein product features automatically

Bug fixes

• Fix a bug preventing gene feature download from some older gene annotation tracks, e.g. for older cow and sheep assemblies
• Corrected errors in protein position reporting in the marker details table for transcripts containing indels relative to the reference sequence
• Fixed bugs in displaying markers in PDF/SVG image downloads
• Fixed a bug in renaming markers from the marker context menu
• Fixed ability to add remote BAM files to graphical display of viral RefSeq molecules
• Fixed inconsistent indel reporting in gene annotation tracks that are older than the current annotation release
• Removed inappropriate download options from the track titles of ORF Finder and Primer-BLAST result tracks

Release Notes for Sequence Viewer 3.36 (April 6, 2020)

New Features and Improvements

• New ability to copy a sequence directly to the clipboard when a range is selected and the view is zoomed to sequence level
• New ability to highlight a sequence range from anywhere in the sequence track by pressing the Ctrl or Command key
• New ability to download track data in BED format from feature tracks such as CpG islands, biological regions, and repeats
• Ability to access track download dialog from the track title of supported track types
• Genes shown in NCBI gene annotation tracks are now weighted by length resulting in a more even distribution map
• Updated to ExtJS v.7.1

Bug fixes

• Fixed a bug in rendering trans-spliced features
• SRA reads in BLAST results can now be viewed in the Sequence Viewer when using the graphics link

Release Notes for Sequence Viewer 3.35 (March 10, 2020)

New Features and Improvements

• Improved adaptive rendering of tabix VCF remote features including reporting features as a heatmap in a zoomed out view
• Improved information in tooltips for uploaded or streamed VCF features
• VCF features will be color-coded by variant type (red for single nucleotide variant, blue for deletion/insertion, yellow for tandem repeat)
• New option to view gaps in the sequence color-coded by gap type (known, unknown, or contamination).
• New ability to go directly to the NCBI Nucleotide or Protein database and view the GenBank flat file by clicking on a menu option under the accession name in the toolbar
• Improved labelling and UX for Reset Tracks button in Tracks Configure menu
• Better rendering of unaligned tails in a zoomed out view of BAM alignment tracks
• All BAM alignment reads are now shown regardless of MAPQ score

Bug fixes

• Fixed incorrect protein sequence reported for immunoglobulin CDS features
• Fixed a bug in downloading sequence from single position markers
• Removed inappropriate links to the Nucleotide database from track title tooltips
• Fixed bugs in the set origin function
• Now showing a more standard sequence track in the viewer found on dbVar record pages
• Additional minor bug fixes

Release Notes for Sequence Viewer 3.34 (January 27, 2020)

New Features and Improvements

• New ability to download data from gene annotation tracks as GFF3, BED, and CSV tables
• Updated the UI of the Download menu on the toolbar (see documentation page Download Sequence and Track Data)
• Added the CDS position to the tooltips for transcript and protein features
• Added the exon number to the tooltips for transcript features
• Added a link to the URL source for remote and hub tracks to the main track configure panel settings display
• Added a link to the URL source for remote and hub tracks to the track tooltip
• Added new tracks for Phenotype and Disease (GWAS data), dbVar data, and Recognition Sites (restriction enzymes) to the tracks configuration menu
• Improved coordination between the ordering of track groupings in the track configure dialog and the order in which tracks are sorted in the graphical display
• Updated help documentation page for Loading External Data and added a demo video for viewing BAM alignment data

Bug fixes

• Fixed problems in the rendering of some alignments in the “Paralogous/pseudo gene alignments” track
• Fixed a bug in the adaptive mode for BED formatted tracks that caused inappropriate rendering as a smear graph (see updated demo page
• Fixed problems with loading tooltips in the Safari web browser
• Fixed problems with viewing data using the Edge web browser
• Restored the ability to place a highlight box around a feature using the binocular button in feature tooltips
• Features that are designated on both strands will no longer be rendered with a directional arrow
• Improved accuracy of language in tooltip and display configuration labels for variation tracks
• Resolved additional minor bugs and performance issues

Release Notes for Sequence Viewer 3.33 (October 10, 2019)

=======================================

New Features and Improvements

• Moved location of downloads options from the Tools menu to a new Downloads menu

Bug fixes

• Fixed display of information in tooltips for MagicBLAST BAM alignments
• Fixed a bug in the hide tracks (X) button in track title tooltips
• Fixed a bug in the use of the back button
• Fixed a bug in setting a track value range using the main track configure menu
• Fixed rendering of some types of features in clone tracks
• Fixed bugs in the “add new panel on range” function

Release Notes for Sequence Viewer 3.32 (September 19, 2019)

New Features and Improvements

• Added ability to download image of the graphical display as an SVG file
• UI updates to printer-friendly download menu (see documentation)
• Reporting of size of a highlighted range in the range selection menu
• Reporting of size of a marker in the marker options menu and in the marker details table
• Added a track configure button to the right end of each track in the graphical display
• Added ability to sort/group BAM file alignment by haplotype tag (see Demo)
• Updates to embedding demo pages
• Improved wrapping of text in tooltips
• Disabled projection of obsolete SNP annotation from Gene features

Bug fixes

• Fixed a bug in embedding SV on third-party pages

Release Notes for Sequence Viewer 3.31 (July 25, 2019)

New Features and Improvements

• Code changes to improve performance
• Updated Sequence Viewer documentation pages, including Legends, Navigating the Sequence Viewer, Interfaces, Tutorials, and Demo pages
• Updated Examples on Demo pages
• Changed the default color for a sequence marker
• Improved interpretation of CIGAR string for BAM files

Bug fixes

• Fixed occasional failures in generation of go.usa.gov short links
• Fixed errors in reporting of coordinates for a component search in the Search Results table
• Fixed errors in reporting of unaligned sequence for alignments displayed on the reverse strand
• Corrected a glitch in the rendering of mismatches in the BAM pile-up graphs
• Improved wrapping of text in Mozilla Firefox
• Fixed bugs in displaying the marker position in Sequence Text View
• Fixed bug preventing rendering of Markers details table in a shared link

Release Notes for Sequence Viewer 3.30 (March 28, 2019)

New Features and Improvements

• Support for tabix VCF remote files
• New display option for graph smoothing for graph tracks
• Improved performance of graphics upon zooming
• Improved performance in moving tracks within the viewer (track drag and drop)
• Improved performance of adding hairlines when features on multiple tracks are selected
• Improved performance of jump to next feature function for remote Bed tracks
• Improved rendering of bidirectional features from remote Bed files
• “Link to View” now uses usa.gov domain
• Updated default track set for standalone Sequence Viewer
• Added new how-to demo videos for adjusting display settings for graph tracks and gene tracks

Bug fixes

• Removed inappropriate “apply to group” option in display settings for non-grouped BAM files
• Fixed bug in displaying coordinate ruler in PDF view
• Brought back sharable link to PDF view
• Fixed issue preventing loading of tracks in the Safari web browser
• Fixed a bug with displaying NCBI SRA files

Release Notes for Sequence Viewer 3.29 (February 13, 2019)

New Features and Improvements

• Implemented the ability to manually adjust the display range of graph tracks
• Propagated the display settings (range, display style, and coloring) provided by track creators of remote track hubs
• Implemented the ability to apply track display settings in bulk to members of a composite track in a track hub
• Implemented the ability to display multiwig files from track hubs
• Updated SV legends and embedding API documentation to reflect updates to graph track display settings
• Added information to tooltips for remote tracks indicating the data is not from NCBI and providing a link to the source of the track
• Improved calculation and reporting of sequence identity and coverage in the tooltips for BAM file alignments
• Added a row reporting intron counts to the alignment statistics table for BAM file alignments
• Added clone name and clone library information to the tooltips for features in the Tiling Path (Components) NCBI track
• Improved performance speed of rendering of NG Alignment track
• Improved default track description text in the display settings for graph tracks

Bug fixes

• Corrected inappropriate display of remote tracks in some embedded SV contexts
• Fixed a bug in displaying unaligned tails for BAM file alignments
• Fixed a bug in showing unaligned tail sequence in the tooltip for BAM file alignment features
• Fixed a bug in displaying primer pairs in the Primer-BLAST graphical view
• Corrected Help link on the Sequence Text View panel
• Corrected errors in some CDS annotations in the Sequence Text View panel
• Fixed bugs in marker options to “Reveal in Graphic view” and “Modify Position/Range/Color”
• Fixed bug in loading the graphical display on Internet Explorer

Release Notes for Sequence Viewer 3.28 (November 13, 2018)

New Features and Improvements

• Remote BAM files can be registered over https://
• Rendering of gaps and introns in BAM file alignments is improved: gaps are colored red as distinct from introns which are colored gray
• Introns and gaps are reported separately in tool tips for BAM file alignments
• Reporting of RNA and protein title, length, and sequence information on tool tips for merged gene features is improved
• Protein sequence and RNA sequence in gene feature tool tips is reported relative to the orientation of the feature
• New tracks can be added without re-rendering existing tracks resulting in improved viewer performance

Bug fixes

• Fixed a bug in using the Find function to set a marker at a sequence coordinate
• Restored “Collapse on a single line” option for SNP tracks
• Fixed errors and improved reporting of gaps in the Match/Mismatch
• Restored reporting of track name in track tool tip for remote BAM files
• Corrected the link to the HGVS database in the Marker details view
• Fixed bug in displaying hairlines of selected features when the strand is flipped

Release Notes for Sequence Viewer 3.27 (September 25, 2018)

New Features and Improvements

• Improved tool tip content for transcript and CDS features including addition of position information
• Updated documentation for Tool Tips
• Improved name reporting in track tool tips for remote bigBed and bigWig tracks
• Added (R) prefix and green highlight to track title for remote tracks from a URL
• Implemented caching to improve time for loading of bigWig track data
• Improved rendering of existing tracks when new tracks are added and the range is not changed

Bug fixes

• Restored loading of Sequence Viewer in Internet Explorer
• Restored ability to search by SNP rs ID
• Fixed bug in processing SNP tool tip content
• Fixed issues with seqconfig in obtaining placement and assembly information
• Fixed bug in marker position in Sequence Text View
• Restored ability to flip strands at high zoom levels
• Restored ability to select multiple features in different tracks
• Fixed bug in removal of tracks using track configutation menu
• Fixed bug in setting new sequence origin

Release Notes for Sequence Viewer 3.26 (August 07, 2018)

New Features and Improvements

• Implemented initial product support for data in UCSC Track Hub format
• Support for displaying remote http/https hosted BED and WIG files
• Improved documentation (legend) for sequence view
• New demo page on how to embed Sequence View to show custom, http:// hosted BAM files
• New demo page on how to embed Sequence View to show custom http:// hosted BigBED and BigWIG files
• Embedding API documentation updated with details for display of remotely-hosted user data

Bug fixes

• Fixed bugs in frame labeling for Six-frame translation
• Fixed performance regression in back-end services, implemented new optimizations for faster graphics
• Fixed issues with accessibility compliance of graphics and UI elements
• Fixed minor issue with track remove button in Slim mode
• Fixed issues in search service (incorrect search for SNPs, crashes, etc)
• Fixed issues with overlaying graphs and charts in one track
• Fixed front-end CSS issues, causing garbled warnings messages on some pages (BLAST)
• Fixed issues with display of uploaded, user defined sequences
• Fixed issues with incorrect tooltips caused by bugs in screen coordinate recalculation
• Fixed issues with PDF rendering of overlay graphs (mislabeling of the data)

Release Notes for Sequence Viewer 3.25 (February 14, 2018)

New Features and Improvements

• New user interface and programmatic API to attach and show HTTP based BAM files.
• BAM coverage graph – added scale display indicator, changed default scale from linear to logarithmic
• Performance optimization for BAM files renderings
• Improved usability of zoom functions added zoom in on mouse double click, smooth zoom, etc.
• Improved tooltip for RNA (ncRNA) features

Bug fixes

• Fixed non-functional tooltips for conservation tracks
• Fixed issues in coloring of BLAST tracks
• Configure dialog: fixed issues with deselecting all active tracks
• Removed obsolete links from CDS popup
• Fixed bug in feature label rendering, making NMs 1bp shorter than it really is
• Variation track: fixed heat map display mode
• Alignment tooltips: fixed issues with unaligned regions (tooltips made sequence position dependent and more robust)
• BAM read tooltips: fixed incorrect mouse over areas (it was a few pixels off)
• BAM alignments rendering: fixed issues with zoom in and out switch between reads and pileup chart, viewer is now capable to display more reads
• Fixed issues with tooltips interference between markers and feature tooltips

Release Notes for Sequence Viewer 3.24 (November 14, 2017)

New Features and Improvements

• API to embed SV and read network placed (http) BAM/cSRA files
• Performance optimization for BAM files renderings
• Improved track names for PrimerBLAST
• Improved track scrolling, added smooth algorithm, improved response time
• Improved rendering of internal unaligned regions, show number of unaligned bases

Bug fixes

• Fixed issues in tooltips processing
• Fixed issue with short URL to view was not always working
• Fixed issues with some SRZ accessions (dbGap studies)
• Fixed issues with track order on reset to default track list
• Fixed issues with toolbar arrow button shift if clicked repeatedly, improved navigation

Release Notes for Sequence Viewer 3.23 (September 19, 2017)

New Features and Improvements

• Improved rendering of bases identical to sequence in alignments
• Performance optimization for alignments renderings
• Improved tooltips in uploaded VCF files

Bug fixes

• Fixed issues with rendering of features projected through alignments
• Fixed issues with some CDS missing in the recently annotated genomes
• Workaround for some scrollbar issues on new browsers using dynamic on demand page scrollbar
• Fixed issues with Feedback for BLAST derived alignments
• Fixed issues with full view and links for BLAST derived alignments
• Fixed rare bug with incorrect translation of peptides due to frame split issues
• Fixed range selection issues in Firefox
• Fixed bug with multiple copies of BLAST alignments appeared

Release Notes for Sequence Viewer 3.22 (July 24, 2017)

New Features and Improvements

• Alignment rendering updated to not render bases identical to reference sequence to enhance clarity. User can select the new display option “Show Identical Bases” to render all bases.
• BAM and cSRA tracks: improved performance of rendering for deep coverage data
• Alignments tracks: strand display improved to be more consistent with the molecule strand when genome is in the antisense orientation
• Improved support of tooltips on touch screen devices, tap on a feature to show tooltip
• Alignments for BAM/cSRA tracks: improved renderings of [mate pairs] (/tools/sviewer/legends/#anchor_7.5)
• Mouse click on track header now invokes Display Options dialog
• Configuration Dialog improved layout of elements for track display options

Bug Fixes

• Fixed back-end issues related to HTTPS/SSL support
• Fixed issues with sometimes missing overview/panorama
• Data upload: fixed tooltip information coming from uploaded VCFs
• Fixed display of 32-bit based graphs

Release Notes for Sequence Viewer 3.21.6 (June 28, 2017)

New Features and Improvements

• N/A

Bug Fixes

• Fixed Ext JS 6.5.0 tool-tip positioning bug

Release Notes for Sequence Viewer 3.21.5 (June 15, 2017)

New Features and Improvements

Switched to use ExtJS 6.5

Bug Fixes

• Fixed issues with sequence track alignment on large displays after scrolling
• Fixed issues with unresponsive sequence text view menu option
• Fixed issues with SNP tooltips
• Fixed issues with "Range" menu
• Fixed issues with feature selection by mouse on touch-enabled devices
• Fixed issues with feedback button
• Fixed issues with range selection in Firefox
• Fixed issues with scroll bar in stand-alone Sequence Viewer in Firefox

Release Notes for Sequence Viewer 3.21 (May 16, 2017)

New Features and Improvements

• Added parameters to define pile-up praph size in BAM files ( demo )
• Improved track hiding (via tooltips) so it does not re-render all other tracks

Bug Fixes

• Fixed issues with touch screen interface on Windows based PCs
• Fixed issue with showing no track instead of empty track, when there is no data
• Fixed issues with protein projection ruler
• Fixed issues with displaying tooltip far SNP rs-ids in the big-int address space
• Fixed issue with SNP label to add allele information
• Fixed issues with feature highlight being misplaced, when feature is at the bottom of a view

Release Notes for Sequence Viewer 3.20 (March 27, 2017)

New Features and Improvements

• Implemented discrete (binned) color maps for graph tracks ( example )
• Improved performance loading tracks for certain highly fragmented molecules
• Improved event API related to change of the visible range, change of list of tracks, etc
• Improved performance of initialization (server side)
• Added [+] symbol to expandable Gene features
• Added status bar at the bottom to better display possible errors, tracks, other information
• Improved display of overlapping variation features

Bug Fixes

• Fixed race condition / crash in the back-end infrastructure
• Fixed bug in projected CDS feature view through alignment
• Fixed tooltips in IE

Release Notes for Sequence Viewer 3.19 (January 24, 2017)

New Features and Improvements

• Implemented new aggregate track type biological_region_track
• Implemented new coloring scheme for some existing feature types
• Improved display of cleaned alignments
• Improved display of projected features, removed unnecessary duplicates
• Improved feature highlight display, cleaned duplicate features when displaying merged or unmerged transcript/CDS pairs
• Added new manual for using embedding API

Bug Fixes

• Fixed issues with user data availability if browsers different than initial upload
• Fixed issues with molecule scrolling
• Fixed configuration issues causing clinical variations on non-human molecules

Release Notes for Sequence Viewer 3.18 (December 5, 2016)

New Features and Improvements

• Improved handling of translation discrepancies
• Sequence track: improved coloring for better reading of sequence/gap distinction
• Improved code generation “Link to this page” dialog for embedding Sequence Viewer on customers page
• Six frame translation track: added new option “Left-to-right translations”
• “Show All” button for gene tracks improved to be more consistent with the track configuration dialog

Bug Fixes

• Fixed “invalid image width” error on some pages
• Fixed issue with not displaying graphics for some submitted sequences on BLAST page
• Fixed issues with garbled characters in track names
• Fixed minor rendering defect (one pixel line) between the ruler and a track
• Fixed issue with Load Defaults
• Fixed issue with next-previous object navigation for gene tracks
• Fixed back-end crash when rendering some variations
• Fixed issue with go to position in sequence text view
• Fixed reverse complement bug in flip strand mode in sequence text view
• Fixed cosmetic issues with extra space sometimes added to graphics
• Fixed issues with incorrect size highlighting for tooltips for mate pairs
• Fixed issues with iframe embedding (size of the iframe was less than needed)

Release Notes for Sequence Viewer 3.17 (October 11, 2016)

New Features and Improvements

• Improved HTTPS compatibility
• Added new toolbar to quickly change Gene track setting to toggle show all features mode
• Changed tracks renderings to show first tracks faster, before all tracks get ready
• Improved display of mixed strand and overlapping alignments
• Tooltip for variant calls now displays "copy number variation"
• Improved embedding API demo to show multiple Sequence Viewer instances in the same space on the page (see Embedding the NCBI Sequence View in Web Content )
• Switched to use ExtJS 6 (fixed multiple issues with ExtJS 5)
• Improved rendering of strand arrows in features to avoid overlap with labels
• Improved rendering of feature selection hairlines

Bug Fixes

• Fixed unnecessary calls to determine genome for local (non-genomic) sequences
• Fixed issues with labels for CDS features
• Fixed minor rendering issues with the ruler
• Fixed issues displaying mixed strand and overlapping alignments
• Fixed issues with slim mode rendering

Release Notes for Sequence Viewer 3.16 (August 29, 2016)

New Features and Improvements

• Improved compliance with HTTPS protocol requirements
• Improved clone tooltips to provide links to evidence
• Improved compliance with coloring instructions from uploaded tracks (BED format)
• New track type: trace data (see Embedding API , Legends )
• Improved labeling for merged gene/mRNA/CDS to avoid duplication of labels

Bug Fixes

• Fixed issues with parameter Orfthreshold for key:six_frames_translation
• Fixed issues with uploading errors after Load Default
• Fixed some issues with GEO uploaded files (WIG format)
• Fixed issues with shifting hairlines for selected objects in some tracks

Release Notes for Sequence Viewer 3.15 (July 12, 2016)

New Features and Improvements

• Feature highlighting improved to support Gene ids
• Improved PDF graphics for markers
• Improved sequence track to better display segment map, recalculate on the fly if needed
• Improved tooltips for merged features, STS, genes and exons, spacing and formatting
• Improved labels rendering for long features
• Embedding API extended to provide functions to change feature highlight colors for tracks

Bug Fixes

• Fixed issues with embedded SV shows 'file is not recognized as five column feature table'
• Fixed issue with tooltips for uploaded track
• Fixed tooltip error issue for alignment track
• Fixed molecule range incorrectly passed to BLAST search
• Fixed tooltip areas overlap for adjacent features
• Fixed issues with [x] track button overlapping with other elements on the same page
• Fixed feature expansion bug when there are two tracks based on the same annotation, but different rendering parameters
• Fixed issue with toolbar gets blocked when user uses it before all tracks are loaded
• Fixed error message appearance in some browsers when incorrect molecule ID was used
• Fixed double tooltip in Assembly menu

Release Notes for Sequence Viewer 3.14 (May 12, 2016)

New Features and Improvements

• Sequence Viewer upgraded the platform to use ExtJS 5. All the embedders may need to review their pages and make adjustments to accommodate new APIs.
• Changed the default rendering option for dbVar track to make it expand child objects upon mouse click
• Improved molecule menu to show new genomic assembly dialog with quick link access to the genome page, provide a quick link to a taxonomy page

Bug Fixes

• Fixed tooltip area overlap on some objects
• Fixed tooltip layout issues

Release Notes for Sequence Viewer 3.13 (April 13, 2016)

New Features and Improvements

• Improved performance how system determines target genome for a molecule
• Internal platform libraries upgrade

Bug Fixes

• Fixed bug with incorrect SNP search for some molecules

Release Notes for Sequence Viewer 3.12 (March 3, 2016)

New Features and Improvements

• Improved rendering for clone placements , evidence data added to tool-tips
• For dbVar, click on variant region toggles display of child calls , evidence data added to tool-tips
• Feature search improved not to include tracks with no visual objects at feature location
• Tool-tips for merged genes improved to include dependent RNA, CDS features
• Improved display of labels for long variation features
• Alignments tool-tips improved to show unaligned tails/ends
• Added an extra sequence coordinate ruler at the bottom
• Implemented multi-marker FASTA download

Bug Fixes

• Fixed some internal issues related to compatibility with Primer BLAST
• Fixed issues with track tool-tips for Clinical Variations and other tracks
• Fixed issues with gray-scale rendering mode in six-frame translation tracks
• Fixed standalone track view function, available in track tool-tips
• Fixed accessibility issue, when viewer has to display info on a missing URL link
• Fixed issues with (non)activation of a sequence track when using zoom to sequence function
• Fixed issue with missing tracks description interpretation
• Fixed formatting issues in some tool-tips, cleaned duplicate links
• Fixed appearance of some dialogues for Linux version of Firefox browser

Release Notes for Sequence Viewer 3.11 (December 08, 2015)

New Features and Improvements

• Sequence viewer can now overlay multiple graphs in one track (for more information please see Demo pages and API documentation )
• Tooltips extended to show all qualifiers
• Improved track descriptions for better integration with track management
• Updated SNP tracks to show newer build
• Tooltips for dbVar (structural variations) improved to include link to the corresponding dbVar study

Bug Fixes

• Fixed track encoding issues my result in track(s) disappearance on some pages
• Fixed track upload data being presented to users who did not requested the data
• Fixed track duplication (Alignments) after a page refresh
• Fixed bug in the configuration dialog, causing button inactivity
• Alignment track – fixed issue with not showing alignment details in some zoom levels (higher magnitude)

Release Notes for Sequence Viewer 3.10.5 (October 20, 2015)

New Features and Improvements

• Added support for track sets with non-default display options

Bug fixes

• Fixed track reordering drug-n-drop bug
• Fixed incorrect marker display, when location is in an intron
• Fixed internal issues with logging and monitoring
• Fixed issues with loading external alignments

Release Notes for Sequence Viewer 3.10 (September 29, 2015)

New Features and Improvements

• Added support for Track Sets and Track Collections (for more information please see My NCBI Track Collections Introduction and NCBI Recommended Track Set Introduction videos).
• Performance optimization, allows faster switching between molecules in genomic browsers and faster Sequence Viewer staging
• Alignment track: new display option added to “Hide Alignments” for duplicate and bad reads
• Track display improved to support larger number of tracks displayed simultaneously in one configured Sequence Viewer
• Improved handling of Fixed Scale parameter of Graph tracks
• Improved to display the product length based on a product_length feature qualifier if feature does not have a known product that can be used to compute the length
• Implemented better detection of nucleotides belonging to a genome assembly to allow configuration and display of more tracks
• Data upload now explicitly shows accession of Genomic Assembly used for the upload
• Flipped strand now generates FASTA download for reverse strand

Bug fixes

• Fixed incorrect requests to display alignments referring some local data
• Fixed errors related to access to certain WGS accessions
• Fixed feature interval comparison (visual hairlines)
• Fixed bug with feature binding areas accuracy
• Fixed issue with range markers interfering with user interface controls (like [x] to hide tracks)
• Fixed bug for changing display parameters for uploaded tracks via URL

Release Notes for Sequence Viewer 3.9 (July 27, 2015)

New Features and Improvements

• Track and data upload API changed to add an option on how to upload data, new embedding parameter “url_reload” added ( see more info
• Upgrade to internal call scheduling infrastructure, fixes some unwanted delays, improves response time
• Improved HTTPS compliance

Bug fixes

• Fixed major issue when all tracks can disappear after some track manipulations
• Fixed bug in Marker Details reports incorrect HGVS positions when indel exists between genome and transcripts
• Fixed issues with intron rendering when data is coming from BAM/SRA files
• Fixed issue with graph scale does not change (Linear/Log) after configuration
• Fixed issue with uploaded tracks not displayed automatically
• Fixed issue with Configure dialog when it was not always applying changed settings
• Fixed incorrect selection length for some features
• Fixed sequence viewer embedding (panorama) mode to ignore track set

Release Notes for Sequence Viewer 3.8 (June 02, 2015)

New Features and Improvements

• Implemented new track navigation GUI to quickly find the next feature like gene, exon, SNP, alignment (also see the video tutorial)
• New API option for color parameter for negative graph values
• Added new button in track tooltip to quickly open this track in standalone view
• Improved variation tooltips for clinical significance

Bug fixes

• Fixed issue with progress bar remained on screen after loading graphics
• Fixed rendering errors (white gaps) in alignment coverage graphs
• Fixed error with showing uploaded data
• Fixed error with a sometimes empty Text View (Tools menu)
• Fixed issue with not showing tracks in certain configurations
• Established back-end guard for fast restart of failed infrastructure nodes
• Fixed failure to modify track display options for uploaded local sequences

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

New Features and Improvements

• Improved performance by rendering multiple data tracks in parallel
• Added scatter plot visualization options ( example )
• Improved renderings of Restriction Sites ( example )
• Improved tooltips for SRA accessions to show CIGAR string

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