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AbXtract™ Module for Sequence Analysis

Analyze your Next Generation Sequencing (NGS) and Sanger data on the cloud with the Orion® molecular design platform. These capabilities are part of AbXtract™, a module within Orion's Antibody Discovery Suite. AbXtract was developed in partnership with Specifica, founded by Andrew Bradbury, PhD, an innovator in novel antibody technologies. Contact us for a demo on how AbXtract can help you obtain potent leads with the most favorable developability and biophysical profiles.

Use AbXtract™ in Orion® to identify antibodies within the same functional cluster that have reduced number of liabilities.

Compared to conventional colony screening methods, NGS screening with AbXtract helps teams:

Uncover more leads. Increase the number of clonotype leads five- to ten-fold compared to random colony screening
Increase sequence diversity and cluster representation. Explore the entire sequence diversity within selected populations, even rare clones that are typically missed by low-throughput methods that favor more abundant antibodies
Prioritize promising leads. Tie in known data, and even low-throughput assay data, to prioritize leads with the most favorable developability and biophysical profiles
Minimize costs. Achieve high throughput for a fraction of the cost of conventional assay runs
Equip the entire discovery team. Automated workflows for novice users, while allowing expert users to fully configure their settings

Antibody discovery projects that were previously out of reach because of software, hardware, computation, or data sharing limitations have now become possible with AbXtract on Orion. -- Andrew Bradbury, PhD, Specifica

From Millions of Sequences to a Select Few

AbXtract has the cloud-based compute power to process tens of millions of sequences into meaningful information. Its sophisticated machine-learning algorithms and workflows help antibody engineers and bioinformaticians parse through this vast amount of data to characterize sequences and extract sequence- and functional-based features. Once promising leads are identified, visual models can further aid in decision-making.

Use AbXtract™ in Orion® to identify antibodies within the same functional cluster that have reduced number of liabilities.

User Friendly

Get Leads from Your Data in Three Guided Steps

Upload sequence files into Orion
- NGS: FASTQ, FASTA
- Low-throughput: FASTA, FASTQ, EXCEL, TSV, CSV
Perform FASTQ quality filtering
Perform simple demultiplexing of highly multiplexed experiments
Annotate to identify CDRs and framework regions of interest (IMGT, Kabat, Chothia, or custom annotation)
Produce annotated records ideally suited for antibody discovery

Extract features
Avoid contaminants
Quantify population statistics
Maximize CDR diversity
Classify functionality
Obtain frequency of clones by population
Eliminate bad sequences (e.g., those seen before or with known biophysical liabilities)
Assess the scaffold distribution
Identify relationships between and within sequence clusters to avoid redundancy
Leverage known data for various sequence populations under different experimental conditions
Look at round-to-round enrichment to identify true binders and better-affinity binders
Couple in low-throughput screening-assay data for sequences with desired features
Identify overlap among different target populations

Identify best performers using NGS metrics derived from experimentally validated studies
Leverage prior knowledge to:
- Maximize diversity
- Reduce risk
- Minimize redundancy
- Optimize time to pre-clinical trials
Maximize the selection of leads with very distinct sequence-based properties
- Perform unsupervised physicochemical clustering to identify clusters sharing similar binding modes
- Easily select unexplored antibodies with likely distinct paratope space
- Identify additional clones that share the same features as those characterized, such as:
  - Antibodies from the same cluster lacking specific sequence liabilities
  - Antibodies from the same cluster that span a broad affinity range
- Quantify developmental liabilities from common and customized references
- Perform region of interest (ROI)-based enrichment calculation across selection rounds / populations
- Identify population overlap at deeper sequencing depth.
  - Identify the relative abundance of clones that bind distinct targets or variants
  - Identify NGS clones that map to already characterized populations

Learn More

Orion’s Antibody Discovery Suite helps you get better leads from your NGS sequence data.

WATCH OpenEye’s miniWebinar recording "Maximizing the Panel of Diverse Leads from a Wide Array of Antibodies Recognizing the Same Epitope with AbXtract™" by M. Frank Erasmus, MS, PhD, Head of Bioinformatics at Specifica, from Thursday, August 25, 2022.

WATCH OpenEye’s miniWebinar recording "How AbXtract™ and Deeper Sequencing can Guide your Antibody Lead Selection and Prioritization" by M. Frank Erasmus, MS, PhD, Head of Bioinformatics at Specifica, from June 16, 2022.