Release notes

Scaligner

• API bug fix: ASASequenceDetails does not require list_altid anymore
• API bug fix: ASASequenceDetails returns cluster information when clusterset_altid is provided
• API bug fix: ASAClusteringDetails

Scaligner

• Improve liabilities identification and reporting:
  • Define new liabilities from the user interface
  • Categorize liabilities (PTM of different priorities, STOP codons, immunogenicity…)
  • Customize the color used to display liabilities (one color by category)
  • Prioritize categories: in case one amino acid is part of several liabilities, the color of the highest priority is used
  • Improve the reporting of liabilities in the Excel sheet. Sheet “PTM and STOP codons” has been renamed “Liabilities”. It has been reworked to contain a list of liabilities for all sequences. Contrary to the previous behavior, liabilities are listed, even if they are not shown in the alignment window. Each liability appears on a row
  • Improve the reporting of liabilities in the Excel sheet => except as above, except that all the liabilities for a sequence in the same cell: eg, “DG in HCDR1, W in HCDR3”
  • Liabilities searched on CDRs will only be displayed if they are entirely contained in a CDR. They used to be displayed on the CDR if the liability was starting in the CDR
• CDR definition
  • Multiple CDR definitions can now be defined for a given numbering scheme and shared at the company level
  • CDR definition are viewable, importable and exportable in the web interface
  • Allow the customization of CDR definitions company-wide (CDR start and stop), eg Kabat CDR1: 27-13 and CDR2 54->12
• Added new numbering positions in Kabat, Chothia and Martin schemes. Several positions present in IMGT and AHo numbering schemes were not present, or only partially present in Kabat and derivatives, which prevent to some antibodies to be aligned. The following position have been added:
  • Kabat, Chothia, and Martin: H9A, H64A
  • Kabat: L54F, L54G, L59A, L66A, L66B
  • Chothia: L54F, L54G, L59A
  • Martin: L52F, L52G, L59A
• Since version 3.27.39, the order of sequences with similar amino acid sequences was not the same in the alignment window and in the Excel file when sequences are sorted by a region. This has been fixed.
• When sorted sequences are exported from the alignment window to an Excel file, the sequence identifier is colored according to the sequence cluster.

Infrastructure

• Server update: PHP 7.4

Scaligner

• BugFix: large deletions (more than 3 bases deleted) in the test sequence were not reported correctly in the Sequence windows, and were preventing other flags from being displayed.

Infrastructure

• Apache version update

Scaligner

• Include numbering labels in Excel file exported from the alignment window.
• Improve Javascript in Web interface to support alignment of 1000+ sequences in reasonable time.
• Add access to “Protocols” and “AB1 import” in the menu bar.
• Enable the customization of the error message email sender to enable relaying in some environments.
• Chromatogram viewer:
  • Merge chromatogram viewer to the sequence viewer, instead of opening a new window
  • Add radio button to select which reading frame to display
  • Add quick help in window to remind the main commands of the editor
• Add NT sequences in a new sheet in Excel file.
• Increase the number of FASTA files that can be loaded at once. Previously Scaligner supported importing one FASTA file only.

Biocorpora

• Enable the storage of several result types for studies loaded without parsing data.