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Alignment

Visualizes the sequence alignment of your antibodies using standard numbering schemes.

This tool is useful for evaluating differences between sequences and for generating IP claims around functional positions.

Accessing the Tool

Select at least one antibody in the Project View. Go to the Analysis menu and select Alignment. This will open the Alignment workspace in a new tab.

Variable Region

Alignment

Constant Region

Alignment Constant

Using the Tool

  • Grouping: Sequences are grouped by chain type (Kappa, Lambda, Heavy).
  • Settings
    • Domains: The Leader, Variable, and Constant regions may be displayed.
    • Numbering and Regions: The numbering and region scheme may be changed by selecting different schemes from their respective selection boxes.
      • Leader sequences are numbered negatively from the start of the variable domain.
      • Constant domains are numbered based on an alignment of the germline sequences for that region.
    • Color Residues: The residues may be colored or not based on ABHAND.
    • Consensus: A consensus sequence may be displayed at the top of each group.
    • Consensus Reference: Select between Calculated Majority (default majority-rule baseline) or any specific sequence entry in the project as the consensus baseline. Selecting a specific entry underlines that sequence's name in the grid and Excel exports. Any section containing chains for that selected entry (e.g. Lambda and Heavy for a Lambda antibody) will use the selected entry's sequence as its consensus baseline and underline the Consensus row label, while sections where the entry is absent (e.g. Kappa) will fall back to calculating section majority with an un-underlined Consensus label.
    • Fade Consensus: Toggle this option to gray out residues that match the selected Consensus Reference, highlighting mutations and unique features relative to the reference sequence or majority consensus.
    • Sequence Logo: Toggle this option to render dynamic stacked amino acid sequence logos above each chain group, displaying position conservation and residue frequency proportions colored by ABHAND.
      • Logo Height (px): Adjust the row height setting (default 84px) directly in the toolbar to scale letter stacks vertically for optimal residue legibility.
  • Linear Sequence: Click the icon next to the entry name to toggle the linear and mature linear number displays above a sequence.
  • Export
    • Export Numbering Sheet: Exports the sequences with all numbering and region depictions.
    • Export Alignment Excel: Exports the alignment in an Excel file.
    • Export Sequence Logos (SVG): Exports multi-chain Sequence Logo tracks (Kappa, Lambda, Heavy) with active primary scheme position numbering and framework/CDR region annotations as a scalable vector graphic (.svg).
    • Export Sequence Logos (PNG): Exports multi-chain Sequence Logo tracks with active primary scheme position numbering and framework/CDR region annotations as a high-resolution PNG image (.png).
  • Engineering Mutation Designs: Click a residue to enter a mutation design used by the Engineering tab.
  • Observations: Click a residue to enter an observation for that IMGT position. These are displayed in the Observations tab and on a clicked residue.
  • Reorder Sequences: Click and drag the grip icon on the left side of a sequence row to reorder the sequences within their chain group. Note that this will also reorder the entry in the chain group for the other chain.
  • Indicator Dots: Dots on a residue position indicate that there is an associated engineering design or observation at that position. Engineering mutations will appear as a small eggshell square while observations will appear as a small orange circle.

Sequence Logos

The Alignment view features interactive, high-resolution Sequence Logos to visualize position conservation and amino acid variation across all aligned sequences.

Features

  • Proportional Letter Stacking: Residue frequencies at each position are represented as stacked amino acid letters scaled proportionally to their occurrence across the aligned set.
  • Automatic 2x Column & Logo Expansion: Enabling Show Sequence Logo automatically doubles the column width from 20px to 40px (44px in exports) and scales the SVG logo letter glyphs 2x wider horizontally using SVG textLength="16.5" (lengthAdjust="spacingAndGlyphs"), stretching every amino acid letter to fill 92% of the column width for crisp, bold, edge-to-edge logos with minimal side margins.
  • Vertical Buffer Separation: Inserted a crisp vertical buffer gap between multi-letter stack items so dark letter outlines remain distinct and separated without merging.
  • Sans-Serif Font Stack & Selective 'I' Rendering: Sequence logo stacks utilize modern sans-serif fonts ("ArialMT", Arial, Helvetica, "DejaVu Sans", sans-serif). Standard letters are scaled horizontally (textLength="16.5") to fill the column width, while Isoleucine (I) is selectively rendered at its natural proportional width centered in the cell so it appears as a clean, crisp, bold vertical bar I without wide box distortion.
  • Dynamic Height Setting: Use the Logo Height (px) control below the Show Sequence Logo checkbox to set custom row heights (default 150px, configurable from 30px up to 200px).
  • Baseline Clipping: Stacked glyphs utilize precision baseline clipping (#logoBaselineClip) so font descender tails (such as Q) sit flush without overlapping adjacent letters or disrupting row margins.
  • Multi-Chain & Region Mapped Exports: Exporting to SVG or PNG generates complete multi-chain figures (Kappa, Lambda, Heavy) mapped with primary scheme position numbering (e.g., IMGT, Kabat) positioned above framework/CDR region header bars (FMWK1–FMWK4, CDR1–CDR3).

Excel Export

Alignment Excel

Numbering Sheet

Numbering Sheet Set

Numbering Sheet Set

Numbering Sheet Entry

Numbering Sheet Entry