Abaligner

Antibody-Extractor Suite

Abaligner is an antibody multiple sequence alignment tool. The algorithm was designed for building alignments based on the 3D structure of immunoglobulin Framework and CDR features.

Features

Abaligner generates three types of alignment layout:

  • Consensus layout: consensus sequence is computed from the most frequent AA at every position.
  • Top Sequence Layout: consensus alignment is built using the first sequence as a template.
  • Plain text alignment.

and three types of alignment output:

  • Html
  • Text
  • Excel

Wu-Kabat variability chart is computed from the alignment and AA and codon position-frequency table is generated.

Scenarios

Scenario 1

Extract and align multiple VH chains from Abi files.

Abi zip file is uploaded to Abaligner. V-Regions are extracted and aligned using Abaligner, the 3D structure based alignment tool. Sequences can be selected and exported from the alignment as text, html or Excel file.

Scenario 2

The patent attorney needs V-Region of VH protein sequences aligned, with Kabat numbering on the top of the alignment. The multiple alignment should be reported in a plain text file.

VH protein sequences file is uploaded to Abaligner. Multiple alignment with Kabat numbering in a plain text file is generated with a single button click.