Annotator

Antibody-Extractor Suite

Whether you process a few or millions of DNA or Protein sequences, Annotator will extract, annotate, remove redundancy and cluster the sequences in annotation groups. Consequently, Annotator will immediately identify the sequences corresponding to functional antibodies.

Features

Annotator checks the quality of input sequences and determines the Frameworks and CDRs coordinates in every sequence. Processed sequences are grouped into different categories:

V-Region: these are good quality and correct sequences. FW1, CDR1, FW2, CDR2, FW3, CDR3 and FW4 are identified and annotated.

V-Genes: FW4 non-annotated.

CDR Len.: sequences are correctly annotated, but CDR length is deviating from user input threshold.

Stop In CDR: sequences are correctly annotated but contain a stop codon in CDR.

Ambiguous: ambiguous AA found in CDR.

FW Not Found: Framework not found.

VGene Not Found: sequences are most likely not immunoglobulin genes.

Can-Cys Not Found: the 2 canonical Cysteines not found. The sequences in this group are most likely not immunoglobulins.

Partial: sequence too short to contain the two canonical Cysteines.

Annotator exports annotated sequences, sequence features in Genbank or Fasta format. Output files are compatible with standard bioinformatics software: Vector NTI, Clone Manager, etc… Highlighted Frameworks and CDRs simplify results interpretation.

Antibody-Extractor uses the most recent technologies from HFT (High-Frequency Trading) field to perform High-Frequency Sequence Analysis. The annotation of 100,000 VH DNA sequences requires less than 30 seconds.

Scenarios

Scenario 1

R&D process generates a large number of VH, VL or VHH sequences. Sequences are processed manually with different bioinformatics tools in a time-consuming and error-prone task. How to improve the productivity of the R&D process?

Annotator uses its proprietary algorithm for finding V-Region or V-Gene. Non-annotated sequences are presented in a way that simplifies results interpretation. Results can be browsed in a browser, downloaded for later interpretation or printed.

Scenario 2

For primer design optimization, non-redundant FW1 DNA sequences should be extracted from a collection of VH ab1 files.

Ab1 files are compressed in a zip file and uploaded to Annotator. Sequences are extracted from ab1 files and annotated. FW1 DNA sequences are retrieved and exported for primer optimization with a single mouse click.

Scenario 3

Lama VH repertoire mining for human-like frameworks.

By setting organism to Homo sapiens and stringency to High, Annotator will mine the Lama VH repertoire for human-like Frameworks.