Query Input
- Query by PDB ID
- Query by antibody features
- Query by sequence
- Query by CH1-CL interface similarity
- Query by uploading repertoire file
User can upload the fasta file containing multiple sequence for search (200 seqs maximum). Example fasta files for both paired and unpaired searching mode are provided to the user, user can click the link to load the example file and search.
Note: In the paired mode, in order to indicate the paired heavy-light chain sequences, the title for the fasta sequence must be in this format: AbName-HorL, where AbName is the name for the H-L pair, HorL can only be the letter of "H" or "L" (case sensitive). The paired sequence must contain the same AbName, with only one H chain and one L chain.
User can upload the repertoire files to VCAb through the following methods: (Please note: to re-upload the repertoire file, please click the "Clear uploaded repertoire file/url" button to clear the previous uploaded file first.)
- Click the "Browse..." button to upload file from your local computer
- Paste a http address of the repertoire file to the box of "Or input a http address for repertoire file here:"
- Send the result calculated by BRepertoire in the "property calculations" panel of the "Analysis" page to VCAb.
Figure above: The "property calculation" panel of the "Analysis" page
Figure above: Click the "Structure analysis" option, and click the button of "Send to VCAb for mapping to antibody structures" to send the table from BRepertoire to VCAb.
Figure above: The BRepertoire page is redirected to VCAb, with the repertoire file from BRepertoire loaded.
VCAb support the following format of repertoire file: AIRR,Cell Ranger, and customized format. Example files for these three formats are provided, and user can view these files by clicking the corresponding link in the Upload repertoire table section on the web page.
For the customized file, it can be any repertoire file format, as long as it contains columns providing these information: amino acid sequence, chain type of the sequence (indicated by the value of IGH/IGK/IGL). Under the paired searching mode, column indicating the cell barcode should also be provided.
After the user upload the repertoire file & select the Customized option as the format, a panel below would be shown:
- When the user select the Unpaired chains as the searching mode
- When the user select the Paired H-L chains as the searching mode
Choose column(s) holding amino acid sequences:
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You can choose one or multiple column(s) holding amino acid sequence here. If multiple columns are choosen, the program will automatically concatenate sequence fragments in these columns into one sequence, and use this sequence for BLAST.This is useful if in the repertoire file, sequences are truncated into fragments of frameworks and CDRs, or fragments of V and C regions.
Note: When multiple columns are selected, the concatenation of fragments depends on the order of the column names you inputed. For example, in the figure above, the sequence used for BLAST search would be fwr1 + cdr1 + fwr2 + cdr2 + fwr3 + cdr3 + fwr4.
Choose column indicating the identity of the chain (IGH/IGK/IGL):
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This column should indicate whether each chain is heavy or light chain. The value of this column can only be one of these: IGH, IGK, IGL. Otherwise thesearch can't be proceed, or the result is inaccurate.
Choose column indicating cell_id/barcode:
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This value is only needed in the paired search mode. This column should hold values unique for each cell (e.g. cell ID or barcode). If one cell contain only one H and one L chain, then the H-L chain is considered paired and will be inputted into the pipeline for searching.