Scaligner is a complete system for antibody sequence analysis, alignment and archival.

Sequences are imported from FASTA files, aligned automatically onto a list of potential scaffolds (eg, germline or protein scaffold) to identify the closest match.

The loading process pairs light and heavy chains and assigns positional numbers to amino-acids.

Scaligner can upload thousands of sequences into the web interface. Users are then able to query the underlying database. For each sequence, regions are identified using user-defined templates and rules, and the sequence is annotated. Scaligner will for instance identify CDRs and framework regions in ScFv sequences.

Scaligner is not limited to ScFv sequence analysis. The process for identifying the regions can be applied both to nucleotide and amino acid sequences, and to any type of scaffold.

The interface provides many key facilities including:

  • Sort sequences by region (CDR1, CDR3…),
  • Mark sequences,
  • Highlight mutations (silent or not), frameshifts and sites of interest
  • Show duplicate regions, silent mutations
  • Analyze residue and length distributions

All sequences can be exported and annotated to EXCEL or FASTA files. Sequences and annotations are stored in a long-term secure database.

Need more details? Contact us! A demo is worth a thousand words.