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Release Notes for MSA Viewer Version 1.25.0 (October 31, 2023)

New Features and Improvements

  • The full page MSA viewer displays an updated header and footer
  • Improved performance due to use of updated technical components (PubSeq Gateway, Stable Components version 28)

Release Notes for MSA Viewer Version 1.24.0 (June 13, 2023)

New Features and Improvements

  • Improved default rendering of MSA Viewer on mobile or small screens
  • Minor tweaks to behavior of alignment info popups

Release Notes for MSA Viewer Version 1.23.0 (February 28, 2023)

New Features and Improvements

Release Notes for MSA Viewer Version 1.22.0 (April 7, 2022)

New Features and Improvements

  • New ability to search for sequence strings in the anchor/consensus row using the Find button on the toolbar

Release Notes for MSA Viewer Version 1.21.0 (November 1, 2021)

New Features and Improvements

  • Gene and protein annotation on the panorama panel can now be hidden using the collape/expand caret button or by adding &collapse_pan to the URL
  • Improvements to display of the toolbar on mobile screens
  • Supports 64-bit NCBI GI accessions

Bug Fixes

  • Fixed sorting of "Identity" and "Coverage" columns in the Rows dialog
  • Additional minor bug fixes

Release Notes for MSA Viewer Version 1.20.0 (March 29, 2021)

New Features and Improvements

  • New option to adjust column width from the Columns configure dialog
  • New ability to access the context menu (e.g. set anchor, hide rows) by right-clicking your cursor over any column
  • New ability to select to highlight a row by clicking within any column; multiple rows can be selected using the Ctrl or Shift keys
  • Warning message added alerting users that MSA currently does not support views of alignments containing both nucleotide and protein sequences

Bug Fixes

  • Additional minor bug fixes

Release Notes for MSA Viewer Version 1.19.0 (January 14, 2021)

New Features and Improvements

  • New option to show columns reporting percent identity, percent coverage, and number of mismatches relative to the consensus or anchor sequence (must show consensus or set an anchor row to see data)
  • New option to show column reporting Gene symbol (for RefSeq accessions)
  • New option to click within the ruler to temporarily set a vertical guideline at a single sequence position
  • Updated data model with improved handling of sequence alignments with large amounts of insertions

Bug Fixes

  • Additional minor bug fixes

Release Notes for MSA Viewer Version 1.18.0 (October 27, 2020)

New Features and Improvements

  • New ability to remove or add columns using the Column dialog found on the top toolbar
  • Option to add columns for country, host, source (isolation source), or date (collection date)
  • Column type and order can be specified in the embedding API
  • Complete text is shown in an information box when you hover over text that is longer than the width of a column
  • Sort rows by column by clicking on the column header

Release Notes for MSA Viewer Version 1.17.0 (September 17, 2020)

New Features and Improvements

  • Additional sorting options in the Rows edit dialog (country, host, isolation source, collection date)
  • New ability to click and drag to selecta region on the ruler above the alignment and zoom directly to that range
  • New ability to download consensus row sequence from the right-click context menu
  • Rows in the alignment can now be selected in bulk using the Shift key

Bug Fixes

  • Anchor row will no longer be shown in the Rows edit dialog as it cannot be hidden
  • Fixed bugs in the behavior of the tooltips
  • Additional bug fixes and tech debt

Release Notes for MSA Viewer Version 1.16.0 (August 10, 2020)

New Features and Improvements

  • New ability to sort columns in the alignment alphanumerically
  • Improved language in reporting insertions and gaps in row position tooltips

Bug Fixes

  • Fixed errors in rendering the ruler for short sequence alignments
  • Fixed ability to download FASTA alignment files from larger BLAST alignments
  • Ambiguous bases will no longer be colored as mismatches in the alignment
  • Additional bug fixes and tech debt

Release Notes for MSA Viewer Version 1.15.0 (July 7, 2020)

New Features and Improvements

  • New ability to hide rows in the alignment from view via the right-click menu or an "edit rows" dialog that can be launched from the top toolbar
  • Hidden rows are not shown in the image or FASTA alignment downloads and are hidden in shared links
  • Shown rows are reported on the status bar on the bottom right of the alignment
  • FASTA download is updated to show the full defline including organism name and title from the GenBank record where available
  • Consensus sequence can be downloaded as part of the FASTA alignment file when the consensus is shown in the view
  • "Master" row is renamed to "Anchor"
  • Updated icon for Tools menu
  • Performance improvements in tooltips from incorporating WebAssembly

Bug Fixes

  • Minor bug fixes

Release Notes for MSA Viewer Version 1.14.0 (May 26, 2020)

New Features and Improvements

Bug Fixes

  • "Show identical bases as dots" checkbox is now shown only when master or consensus is set
  • Ambiguous bases will no longer be counted as mismatches in the alignment or panorama view
  • Additional minor bug fixes

Release Notes for MSA Viewer Version 1.13.1 (May 4, 2020)

New Features and Improvements

  • Added an option in the Tools menu and right-click context menu to show/hide a consensus row
  • The query sequence will be automatically set as master for alignments coming from NCBI BLAST
  • Coloring options for alignments can now be accessed from the top toolbar

Bug Fixes

  • "Show identical bases as dots" works when either a consensus or master is set
  • Fixed a bug in the back button
  • Fixed an image rendering issue when using "Column Quality Score"
  • Fixed a bug in coloring menu options for uploaded nucleotide files
  • Additional minor bug fixes

Release Notes for MSA Viewer Version 1.12.0 (March 30, 2020)

New Features and Improvements

  • Ambiguous nucleotides or residues ('N' or 'X') are now excluded in score calculations and colored dark grey when using the "Frequency Based Difference" and "Column Quality Score" coloring methods

Bug Fixes

  • Fixed isses that resulted in errors in the multiple alignment of SARS coronavirus 2 sequences at the NCBI Virus data hub
  • Fixed ability to view SRA alignments from BLAST in the MSA viewer
  • Fixed link from SRA reads in alignments to the SRA database

Release Notes for MSA Viewer Version 1.11 (January 16, 2020)

New Features and Improvements

  • Added support for stop character * in uploaded FASTA alignment files
  • Added support for pipe | symbol in id of uploaded FASTA alignment files

Bug Fixes

  • Fixed bugs in coordination of panorama and alignment views
  • Fixed glitches in rendering of the master row
  • Fixed bugs in rendering results in COBALT

Release Notes for MSA Viewer Version 1.10 (March 19, 2019)

New Features and Improvements

  • “Link to View” now uses usa.gov domain

Bug Fixes

  • Fixed issue with PDB ID in GI-less database

Release Notes for MSA Viewer Version 1.9 (October 25, 2018)

New Features and Improvements

  • Flexible vertical space allocation implemented

Bug Fixes

  • Projected features in proteins fixed
  • Labels on genomic alignments fixed
  • Upload data option from Tools menu fixed

Release Notes for MSA Viewer Version 1.8 (April 19, 2018)

New Features and Improvements

  • Navigation toolbar improved with capabilities to project features
  • Implemented scrolling of alignments within the MSA Viewer dedicated area
  • Implemented new coloring for CDS alignments to show non-synonymous nucleotide codons (menu Coloring)
  • Tooltips usability improvement – tooltip popup logic made less aggressive
  • Improved scrolling/positioning to use smooth animation
  • Improved tooltip content to better explain consensus symbol and correctly show ambiguous consensus bases
  • Improved feature projection for alignment with local features
  • Improved accessibility (508) compliance

Bug Fixes

  • Fixed production crashes related to back-end OpenGL (MESA) initialization
  • Fixed incorrect column statistics in tooltips
  • Fixed issue with Organism name not being shown for some data
  • Fixed issues with setting Master sequence on some data sets
  • Fixed double appearance for tooltips
  • Fixed issue with ‘X’ character in protein alignments and ‘X’ in consensus

Release Notes for MSA Viewer Version 1.7 (December 28, 2017)

New Features and Improvements

  • Added navigation toolbar with pile-up graph with variation and coverage histogram
  • Added API to hide strand column for DNA alignments
  • Context (right-click) menu improved for usability
  • Major rendering engine upgrade to support large size alignments without limits on projected feature row expansions
  • Usability improvements to make alignments more readable: larger fonts, option not to display matching (consensus) letters, etc.
  • Improved performance of back-end consensus calculations

Bug Fixes

  • Fixed issue with incorrect URL parameters processing for the master/anchor row
  • Fixed front-end issues with unsetting default master/anchor row
  • Fixed bug with master not shown in the consensus=false mode
  • Fixed visual glitches with stand indicator, (+) button, etc.
  • Fixed some browser compatibility issues
  • Fixed issues with the ruler rendering and behavior

Release Notes for MSA Viewer Version 1.6 (June 27, 2017)

New Features and Improvements

  • Switched to use Ext JS 6.5
  • Added ability to download alignment in FASTA format
  • Warning added for missing appname parameter

Bug Fixes

  • Fixed tool-tip information shifting for DNA alignment
  • Fixed tool-tip opening over menu
  • Fixed feedback link
  • Fixed wrong position of the tool-tip when scrolling the page
  • Fixed selection on event processing demo in Chrome and Firefox

Release Notes for MSA Viewer Version 1.5 (April 18, 2017)

New Features and Improvements

  • Added status bar
  • Added context menu to provide links to Entrez to sequences in the alignment

Bug Fixes

  • Fixed issue with not showing species name for uploaded alignment
  • Fixed sudden back-end crash
  • Fixed issues with alignments based on local sequences
  • Fixed incorrect error handling in the back-end
  • Fixed various issues with the demo pages

Release Notes for MSA Viewer Version 1.4 (February 21, 2017)

New Features and Improvements

NONE

Bug Fixes

  • Fixed issue with blank space when zoomed in on some alignments from BLAST under condition, that the Master alignment is set
  • Fixed incorrect tooltip information
  • Fixed issues with showing FASTA alignments with gaps produced by MUSCLE
  • Fixed IE issues with Upload dialog
  • Fixed zooming problem when Master alignment is on the negative strand
  • Fixed issues with text import via clipboard paste
  • Fixed issues with text and labels renderings (scrambled unreadable text)

Release Notes for MSA Viewer Version 1.3 (January 23, 2017)

New Features and Improvements

Bug Fixes

  • Fixed issue with zoom and position loss when user changes the master sequence

Release Notes for MSA Viewer Version 1.2 (December 26, 2016)

New Features and Improvements

Bug Fixes

  • Fixed critical issue on touch screen enabled devices
  • Fixed insertion appearance for BLAST alignments with no master
  • Fixed issues with the ruler length when new master row is picked
  • Fixed conflicts with context menu and tooltips in IE and Safari browsers
  • Fixed issue with image drift on color scheme change

Release Notes for MSA Viewer Version 1.1 (September 27, 2016)

New Features and Improvements

  • New improved rendering mechanism for displaying projected features
  • Improved navigation over gaps in alignments
  • Improved security and compatibility with HTTPs protocols

Bug Fixes

  • Fixed number of navigation issues, related to zoom levels
  • Fixed issues with organism names for some imported alignments
  • Fixed issues with not showing features on protein alignments
  • Fixed various tooltip issues

Release Notes for MSA Viewer Version 1.0 (June 27, 2016)

New Features and Improvements

Bug Fixes

  • Fixed number of browser compatibility issues

Release Notes for MSA Viewer Version 0.1 (May 24, 2016)

New Features and Improvements

  • Multiple Sequence Alignment Viewer is a new product which shows multiple alignments in a Web view
  • It can be embedded in your page by using Embedding API
  • It supports several data formats: NCBI ASN.1 alignment and Genome Workbench Project, MUSCLE (FASTA alignment) is being implemented

Bug Fixes

  • As this is the pilot version there are no bugs identified yet

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Last updated: 2023-10-31T16:58:16Z