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Applications

Use cases

The PipeBio platform integrates powerful bioinformatics tools for fast antibody, TCR, and peptide sequence analysis

Users

Use PipeBio through an easy-to-use interface or integrate with bioinformatics pipelines

NGS and Sanger analysis

See tools for end-to-end antibody sequence analysis

Antibody discovery

An illustration of an IgG antibody with sequence-based liabilities and post-translational modifications shown in the CDRs, C-regions and FRs of the antibody

Identify antibody liabilities and PTM sites

De-risk antibody development by identifying sequence-based liabilities and flagging sequence motifs of residues that may give rise to PTM and affect the structure and function antibody candidates.

Cross reactive antibody clones from 10x genomics BEAM experiment displayed on Phylogenetic tree dendrogram on PipeBio Bioinformatics antibody sequence analysis platform.

Clonal hit expansion

Use PipeBio for mining NGS repertoires for expanding potential hit sequences of characterized antibody sequences

NGS analysis

Volcano plot showing enriched clonal families in antibody discovery biopanning experiment and table with ELISA and other binding assay data on PipeBio Bioinformatics Cloud

Analyze NGS from antibody library, repertoire sequencing, biopanning

Annotate and cluster NGS data from biopanning experiments and find differentially enriched sequence clusters across multiple panning rounds.

Two screenshots of the PipeBio bioinformatics platform showing a sequence alignment of antibodies and a phylogenetic representation of the heavy chain IgG sequences as well as PipeBio's tool that finds the most diverse antibody sequences in a sequence alignment

Identify enriched and diverse antibodies with good binding properties

Add functional assay data, such as ELISA, FACS and other immunoassay data and use built-in tools to identify the most diverse antibodies for synthetization and characterization

Sanger sequences

Sanger sequences of antibodies with chromatograms, annotated CDR and FR regions, amino acids and heterozygous bases identified

Easy Sanger analysis

Trim, assemble forward and reverse reads, detect heterozygous peaks, annotate, edit and align Sanger sequences

Antibody engineering

Antibody 3d structure, hydrophobicity and antibody aggregation prediction

Calculate protein properties and show hydrophobic regions

Use built-in tools to calculate charge, isoelectric point (pI), molecular weight and identify hydrophobic regions in your antibody or peptide sequences

Bulk restriction cloning tool showing insertion of a sequence into vector and Sanger sequences analyzed for antibody engineering on PipeBio

Sequence editing editing, codon optimization

Bulk clone many insert fragments in one simple operation, Identify problematic internal cut sites, edit your sequences in-line in the editor, export to excel, genbank, QPIX.

Scientists

PipeBio Main user interface with sequence alignment of IgG heavy chain and amino acid bar chart

Tools for easy sequence analysis and visualization

PipeBio has a simple user interface and easy-to-use tools to analyze and visualize your antibody sequences

Bioinformaticians

Workflow editor and yaml file for creating custom bioinformatics analysis workflows on PipeBio

Integrate, build automated workflows and manage data

Use PipeBio's flexible tools, scalable compute and data storage capabilities to build and optimize workflows

Tools for sequence
analysis

Accurate Annotation Engine

  • Identify and correct truncated framework regions
  • Detect frame shifts
  • Flag liabilities defined by your preferences as errors and warnings
  • Flexible support for numbering schemes and annotation definitions, including IMGT, Kabat, Chothia

IgG, VHH, scFv, BCR and TCR sequence analysis

  • Flexible support for IgG, Fab, Nanobody (VHH), linkers for ADCs, affibodies
  • Both for synthetic libraries and naturally occurring sequences.
  • Annotate CDRs, FRs, V-gene, J-gene, C-gene, α-chain, β-chain, VH, VL
  • BCR and TCR repertoire sequencing analysis

Custom Germline Database

  • Annotate sequence with any germline, including llama, mouse, rabbit, rat, canine, human and more
  • Works just as well on synthetic libraries and naturally occurring sequences
  • Flexible support for numbering schemes and annotation definitions, including IMGT, Kabat, Chothia
Volcano plot showing enriched clonal families in antibody discovery biopanning experiment and table with ELISA and other binding assay data on PipeBio Bioinformatics Cloud

Cluster & Compare sequences

  • Define your clonotype by cluster on germline, FR, CDR-H or CDR-L, C-regions or across entire VH and VL chains
  • Examine sequence diversity in samples and individual clusters
  • Dive deeper inside interesting clusters and clonotypes
  • Compare samples with tens of millions of sequences from antibody repertoire sequencing, biopanning, phage display
Chart showing antibody clustering of related antibody clones based on CDRH3 similarity

Visualize phylogeny, clusters, enrichment, frequencies and more

  • Use the phylogenetic tree to visualize antibody clonotypes with functional assay data to find ideal sequences
  • Use interactive charts to quickly find sequences by specific residues in certain positions, relevant clusters and more
Phylogenetic tree dendrogram in antibody repertoire analysis

Fast NGS and Sanger sequence analysis

Highly parallelized cloud computing allows you to get results, fast:

  • Analyze billions of sequences (up to NovaSeq) in a couple of days
  • Tens of millions of NGS reads in hours
  • Hundreds of thousands of NGS reads in minutes
  • Hundreds of Sanger sequences in minutes

Supported sequences and file formats

  • Analyze data from Illumina (NovaSeq, NextSeq, MiSeq, iSeq)
  • 10x Genomics single-cell sequencing support
  • PacBio and soon Oxford Nanopore
  • Supported file formats range from Ab1, Fastq, Fasta, Genbank to CSV and Excel (both import and export)

The integrated cloud software for antibody sequence analysis