Cluster (AbScan) Antibody Binding Regions - AbXtract

Category Paths

Follow one of these paths in the Orion user interface, to find the floe.

  • Solution-based/Biologics/Antibody Design

  • Role-based/Bioinformatician

  • Role-based/Biologist

  • Product-based/AbXtract


Clusters sequence using AbScan (default), 100% homology, or edit distance (Levenshstein or Hamming) criteria, with option to condense using biophysical conversion to reduce the dataset from 20 AAs to 11 using underlying physicochemical properties (e.g. aromatics, small aliphatic, etc).

Parameter title in user interface (promoted name)

  • Output Name of Dataset with Clustered Outputs (data_out) type: dataset_out: Dataset of sequences with sequences classified by cluster.
    Default: abscan_cluster

Parameter title in user interface (promoted name)

  • Failed Dataset Output Name (data_out) type: dataset_out: Contains failed records from both upstream and downstream Processes
    Default: problematic.abscan

Parameter title in user interface (promoted name)

  • Clustering Type (cluster_type) type: string: Cluster type to apply to sequencing dataset
    Default: AbScan
    Choices: AbScan, Unique Only, Levenshtein Distance, Hamming Distance

Parameter title in user interface (promoted name)

  • Keep Only Functional Sequences (filter_functional) type: boolean: Eliminates non-functional sequences, truncations, stop-codons, frame-shifts.
    Default: True

Parameter title in user interface (promoted name)

  • Region of Interest For Clustering (roi) type: string: Indicate the region of interest (ROI) for processing. If Illumina, will only use upstream ‘cdr3_aa_1’ for clustering for AbScan, Levenshtein and Hamming. If option ‘Unique Only’ with Illumina, will condense according specified ROI according to chain_1.
    Default: CDR3 Chain_2 (Downstream Chain)
    Choices: Merged CDRs, CDR3 Chain_1 (Upstream Chain), CDR3 Chain_2 (Downstream Chain), HCDR3 and LCDR3, Full-Length

Parameter title in user interface (promoted name)

  • Output CSV Filename (file_name) type: file_out: All records are written to downstream csv file, must contain the csv extension
    Default: abscan_cluster.csv