How to run a Paratyping Analysis

How to run a Paratyping job

• Step 1. On the LensAI™ Home Page, click "Run Analysis"
  

• Step 2. Locate the Paratyping analysis and click "Run Analysis"

• Step 3. Inside the run configuration, select an input file from datasets. 
  
  Two input file types are supported: CSV and FASTA.
  

Either a CSV file or a FASTA file should be selected.

Input CSV file: The preferred CSV format includes the following columns:

• • protein_name
  • chain_name (VH indicating heavy chain or VL indicating light chain)
  • chain_sequence (the sequence string)

Each row represents a single chain of a protein. Sequences that share protein_name are taken together as a single (multimeric) protein.

Example of a valid input CSV file:

protein_name,chain_sequence,chain_name
ab1,EVQLVESGGGLVQPGRSLRLSCAASGFTFDDYAMHWVRQAPGKGLEWVSAITWNSGHIDYADSVEGRFTISRDNAKNSLYLQMNSLRAEDTAVYYCAKVSYLSTASSLDYWGQGTLVTVSS,VH
ab1,DIQMTQSPSSLSASVGDRVTITCRASQGIRNYLAWYQQKPGKAPKLLIYAASTLQSGVPSRFSGSGSGTDFTLTISSLQPEDVATYYCQRYNRAPYTFGQGTKVEIK,VL
ab2,QVQLVQSGAEVKKPGASVKVSCKASGFNIKDTYIHWVRQAPGQRLEWMGRIDPANGYTKYDPKFQGRVTITADTSASTAYMELSSLRSEDTAVYYCAREGYYGNYGVYAMDYWGQGTLVTVSS,VH
ab2,DIQMTQSPSSLSASVGDRVTITCKTSQDINKYMAWYQQTPGKAPRLLIHYTSALQPGIPSRFSGSGSGRDYTFTISSLQPEDIATYYCLQYDNLWTFGQGTKVEIK,VL

Input FASTA file: The FASTA file should include each chain as a separate record:

• • Headers must end with _VH for heavy chains and _VL for light chains.
  • Both chains of the same antibody must share the same base name (e.g., Ab1_VH and Ab1_VL).

Example of a valid FASTA file:
>Atezolizumab_VH
EVQLVESGGGLVQPGGSLRLSCAASGFTFSDSWIHWVRQAPGKGLEWVAWISPYGGSTYYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARRHWPGGFDYWGQGTLVTVSS
>Atezolizumab_VL
DIQMTQSPSSLSASVGDRVTITCRASQDVSTAVAWYQQKPGKAPKLLIYSASFLYSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQYLYHPATFGQGTKVEIK
>Bapineuzumab_VH
EVQLLESGGGLVQPGGSLRLSCAASGFTFSNYGMSWVRQAPGKGLEWVASIRSGGGRTYYSDNVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCVRYDHYSGSSDYWGQGTLVTVSS
>Bapineuzumab_VL
DVVMTQSPLSLPVTPGEPASISCKSSQSLLDSDGKTYLNWLLQKPGQSPQRLIYLVSKLDSGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCWQGTHFPRTFGQGTKVEIK

• Step 4. Define options
  
  • Select “VHH” if the input sequences are nanobodies. Otherwise select “IgG Fv”.
  • Define “Target name” to be used in the report.
• Step 5. Define the output dataset logical name
  
• Step 6. Optionally provide experiment details under the General Run Metadata Inputs
  
• Step 7. Click "Run Analysis" to launch the application
• Step 8. Monitor the analysis state and results in the "Analyses history" sidebar