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