Scaligner™ Software Platform

Slide Automate sequence alignments according to your choice of numbering scheme (Kabat, IMGT, Chothia, Aho, Martin) Slide Identify the closest germlines Slide Visualize frameshifts, mutations, post-translational modifications and stop codons by color-code Slide Cluster sequences by selected CDRs or framework regions Slide Sort your sequences by similarity to a given sequence or group sequences with identical regions Slide Evaluate sequence humanness

Automate sequence alignments. Perform pairwise (or multiple) sequence alignments to determine the relatedness of a pair (or a mutiple) of sequences, e.g the sequence of an uncharacterized immunoglobulin sequence to the sequence of a related reference sequence or germline sequence, all within the same interface you use for post-alignment analysis.

Scaligner™ makes it easy to further explore the relatedness of pairs of sequences from multiple alignments, align transcripts to genes, or find a gene within a genome.

The reliable assignment of rearranged immunoglobulin genes to their respective germline alleles is an important first step in the analysis of antibody repertoires, to determine germline gene usage, as well as to help characterize clonotypes within the repertoire.

Visualize frameshifts, mutations, post-translational modifications and stop codons by color-code. Scaligner™ identifies mutations, and patterns in sequences such as potential post-translational modification sites and stop codons during the automated analysis process. Mutations, PTMs and stop codons are highlighted by color and are immediately recognized.

Cluster sequences by selected CDRs or framework regions. Sort your sequences by the region of interest (e.g. CDR or framework region). Scaligner™’s built-in sequence similarity computation tool identifies “homologous” proteins by comparing amino acids at equivalent positions according to the numbering scheme and groups those sequences into clusters.

Identify the closest germlines. A full repertoire of germlines for multiple species (human, mouse, rabbit, dog…) is already part of the Scaligner™ database. In addition, Scaligner™ allows you to create, manage and import your own set of germline sequences.

Scaligner™ automatically detects light and heavy chains within a sequence, identifies the closest germlines from its germline database (or your own imported sequence set) and computes sequence homology in respect to the germline. Amino acid/Nucleotide similarity is reported as similarity score.

Scaligner™ is not limited to only ScFv sequence analysis. The process for aligning sequences can be applied to any type of protein scaffold.

Identify CDRs and framework regions. Scaligner™ automatically identifies Complementarity-determining regions (CDRs) and framework regions in scFv sequences. CDRs and FRs are defined based on the selected numbering scheme or they can be user-defined.

Evaluate sequence humanness. Scaligner™ evaluates sequence humanness by a score system (H-score, G-score, T20 score, germinality index). Scores are displayed in the sequence window. They are represented along with a distribution of scores of human mouse antibodies to estimate how “human” the sequence is.

Next Generation Sequencing Module

The NGS analysis module integrates into your Scaligner™ software pipeline. Its powerful cloud computing platform will assist you to align millions of DNA sequences and extract actionable information from your sequence data at high speed.


  • Analyze millions of NGS raw antibody sequences within minutes
  • Annotate and compare NGS sequences without manual intervention
  • Search and filter on large NGS datasets
  • Cluster and index annotated NGS sequences
  • Show cluster diversity and region length plots
  • Base algorithms: FR/CDR identification, germline identification, germline grouping, unique sequence count, similarity and clustering


  • Compare clonotypes from different NGS data sets
  • Inspect individual sequences in large data sets using the intuitive sequence viewer
  • Plot diversity of residues and amino acid frequencies for specific positions for a dataset and for individual germlines
  • Plot CDR length distributions
  • Look at amino acid variability with composition plots


  • Spot high-level trends in large scale antibody NGS datasets
  • Drill down into individual sequences
  • Achieve deep understanding of your antibody data
  • Accelerate precision antibody discovery

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Data Management and Storage

Data management usually requires a huge initial investment – one reason why many smaller businesses hesitate to go for a data management solution, even if they strongly feel they should. Scaligner™ securely archives your sequences including your raw data, sample annotation and analysis results in your in-house repository with access right management.
No need for a dedicated database specialist on your site!

Sequence list management. Classify and store your sequence data in lists to facilitate access, review and easy management of sequences such as duplicating, renaming, changing or deleting.

Teams & access levels. Organize your employees in teams and set group permissions or give individual access levels, where needed.

Shared folders. Optimize your teams’ workflow with organized shared folders to control data access in and outside the company. Share projects securely with collaborators without requiring file downloads.

Comments to files & folders. Take the opportunity to comment on files to ease user collaboration and skip using unsecured chat platforms.

Activity monitoring. Have all of your account activity recorded in detailed logs and access any previous versions of your files.

Scalable system. From a few users up to company-wide installation, Scaligner integrates to your corporate environment for access right and user management. Scaligner™ easily sets up to your business requirements.

Enhanced search. Search the contents of your projects and find sequence files the way you remember them, either by name or by sequence.