Use cases

Discover the Antibody-Extractor use cases and the challenges our customers have addressed

The manual processing of a large number of VH, VL, VHH or scFv sequences with different tools is a time-consuming and error-prone task.

You can improve your productivity by using Annotator. Its proprietary algorithms finds the V-Region or V-Gene. Non-annotated sequences are presented in a way that simplifies results interpretation. Results can be viewed in a browser or downloaded for later interpretation.

For primer design optimization, non-redundant FW1 DNA sequences need to be extracted from a collection of VH ab1 files. A tedious process.

Simply upload your compressed Ab1.  Annotator will extract sequences from the ab1 files and annotate them and export FW1 nucleotide sequences with a single mouse click.

Mining a non-human repertoire for human-like frameworks is a heavy task.

Just set the organism to “Homo sapiens” and have a couple of runs with various settings for stringency, and Annotator will mine the complete non-human VH repertoire for human-like Frameworks in minutes.

Determining the immune diversity of your antibody library is not a trivial task.

The Abcluster algorithm will process your dataset through multiple clustering cycles and generates output results help assess the library diversity.

You need to find the highly expressed VH in your immune repertoire?

Just upload you’re your NGS library to Abcluster and it will find and sort the highly expressed chains clusters in one go.

You want to find out how VH chains with the same CDR3 evolved from their germline V-Gene?

Trust Abcluster to cluster VH chains with the CDR3 and the appropriate germline V-Gene.

You need to extract and align multiple VH chains from Abi files.

Just upload your Abi zip file to Abaligner. V-Regions are extracted automatically and are aligned using the 3D structure-based alignment tool. Select your sequences and exported them as text, html or Excel file.

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

Once your VH sequences are uploaded to Abaligner, you obtain the full alignment with Kabat numbering in a plain text file with a single mouse click.

You want to know the V-Gene frequency usage of your NGS dataset of functionally active antibodies.

Submit your DNA sequences to Germaligner. V-Region or V-Gene protein sequences are extracted from the dataset and processed. Antibodies from the same germline are grouped into clusters and aligned using Abaligner.

You want to perform a Germline-based humanization of non-human antibodies.

Germaligner will generate a 3D structure-based alignment of your antibody sequences with germlines genes in a user-friendly interface to assist you with your decision making during the humanization processes.

You selected your VH clone of interest, but you wonder if there may be another similar clone in the immune repertoire?

Rely on Abquery to mine the repertoire and find sequence variants. The algorithm displays the results as multiple alignments with statistical data in a visually effective way.

Before the humanization of a VH sequence, you want to check if the required mutation occurs naturally in similar VH clones from the same immune repertoire.

Let Abquery find similar VH sequences. Next, Abaligner will align the sequence hits with the query VH as a consensus sequence. Mutations are clearly visualized in the alignment and the Wu-Kabat variability and the amino acid position-frequency data are generated.

You need to compare two NGS datasets, Library “A” and Library “B”, to find enriched sequence clusters.

Upload your libraries (they may contain millions of sequences) and let the Pan4Seq algorithm compare them. The algorithm will sort the enriched ones according to specific Pan4Seq parameters and generate a user-friendly report. The approach can also be used to compare two patient populations, “control” and “test”, to find a specific immune fingerprint for a certain pathology.

The antibody discovery team wants to check if there is a candidate for intracellular delivery in their antibody collection.

Let MotifFinder screen the 1200 VH sequences for Endosomal Escape Domains (EED) and extract the VH chains with this EED signature. MotifFinder shows in which feature, Framework or CDR the EED are found.

After humanization, you need to find quickly specific amino acids or codons at a determined position in VH protein or DNA sequences.

Starting with DNA VH sequences the Hotspot algorithm computes the amino acid and codon Wu-Kabat variability. Variability is reported as charts, and the raw data is exported in Excel format for further processing.

How to check for restriction sites inside the V-Region and in-silico batch clone 192 VH chain sequences in a plasmid?

Provide Abcloner with the following input: The Plasmid and 1 or 2 restriction enzymes. Abcloner will annotate the 192 VH sequence, search for restriction enzymes then cut and extract the V-Region fragment, that will be inserted into the plasmid. The new construct is annotated, and the plasmid features are shifted, taking into account the V-Region insert size. Constructs are reported in a downloadable multiple Genbank file.

Abparam & Protparam
The protein purification team wants to validate the hypothesis that the poor purification of some Nanobodies is related to their low isoelectric point.

The Nanobodies DNA or protein sequences are uploaded into Abparam. All the relevant parameters are calculated and Abparam filter extracts Nanobodies with a low pI and reports the results in Excel format. In a couple of minutes the scientists were able to confirm their hypothesis. All the poorly purifiable Nanobodies were exported in the Excel table for further follow-up work.

A BAC with unknown Llama VH germline genes was sequenced using Ion-Torrent technology. After the assembly of the 600,000 Ion-Torrent reads of about 120 bp, Llama VH germline genes had to be identified for the first time and extracted from the assembled contig.

gExtractor, a ,machine learning algorithm,  finished the job in a single run.

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Learn more about our “in-vitro maturation” concept: Combining phage display with NGS for the discovery of potent antibody variants. An argenx use case.