VDJGermline v3
1 Introduction
VDJGermline is a bioinformatics-based tool for antibody sequence VDJ analysis. Through sequence alignment, it can quickly retrieve the most homologous sequences to the target antibody sequences from a rich VDJ gene library, and deeply analyze the VDJ gene rearrangement information. It is particularly suitable for the sequence analysis of animal immune repertoires. The gene library covers multiple species, including humans, mice, rhesus monkeys, and camels, and has specifically constructed the “HUGO H3K3” fully humanized mouse gene library. It outputs analysis result tables for each sequence, visual alignment charts, and a variety of statistical analysis charts.
2 Parameters
- Sequences: Input protein sequences or DNA sequences.
- Species: Select the species to match. Choose from the following options:
- Match: Identify the most similar species. Note that species matching is not 100% accurate; if the species is known, please select the known species.
- Human: Matches human VDJ genes (Homo sapiens).
- Alpaca (H): Matches alpaca VDJ genes (Vicugna pacos).
- Mouse: Matches mouse VDJ genes (Mus musculus).
- Rat: Matches rat VDJ genes (Rattus norvegicus).
- Rhesus Monkey: Matches rhesus monkey VDJ genes (Macaca mulatta).
- Rabbit: Matches rabbit VDJ genes (Oryctolagus cuniculus).
- Pig: Matches pig VDJ genes (Sus scrofa).
- HUGO H3K3: Matches the HUGO fully humanized mouse VDJ genes.
- Chain type: Specify the type of chain to be identified. Choose from the following options:
- Match: Identify the most matching chain.
- Heavy: Identify only the heavy chain.
- Light: Identify only the light chain.
- Cgene Species: Specifies the species for matching the C gene. Choose one of the following:
- Human: Matches human C genes (Homo sapiens).
- Mouse: Matches mouse C genes (Mus musculus).
3 Results Explanation
- Table: Germline results summary table, supports CSV format download.
| Field | Description |
|---|---|
| query_name | query name. |
| sequence | DNA sequence. |
| sequence_aa | Protein sequence. |
| locus | Chain type(H,K,L). |
| organism | Species. |
| v/d/j_call | V/D/J gene that matches the sequence. |
| sequence_alignment | DNA sequence aligned with homologous DNA sequence. |
| germline_alignment | Closest matching homologous DNA sequence. |
| sequence_alignment_aa | Protein sequence aligned with homologous protein sequence. |
| germline_alignment_aa | Closest matching homologous protein sequence. |
| v/d/j_sequence_alignment | V/D/J gene DNA sequence of the DNA sequence. |
| v/d/j_sequence_alignment_aa | V/D/J gene protein sequence of the protein sequence. |
| v/d/j_germline_alignment | V/D/J gene DNA sequence of the homologous DNA sequence. |
| v/d/j_germline_alignment_aa | V/D/J gene protein sequence of the homologous protein sequence. |
| fwr1/2/3/4 | FWR1/2/3/4 region sequences of the DNA sequence. |
| fwr1/2/3/4_aa | FWR1/2/3/4 region sequences of the protein sequence. |
| cdr1/2/3 | CDR1/2/3 region sequences of the DNA sequence. |
| cdr1/2/3_aa | CDR1/2/3 region sequences of the protein sequence. |
| v/d/j_score | Matching score of V/D/J. |
| v/d/j_identity | Identity of matching for V/D/J. |
| numbering | IMGT Numbering of the protein sequence. |
| cdr1/2/3_number | IMGT Numbering of CDR1/2/3 regions. |
| mismatch_aa | Number of mismatches with homologous protein sequence. |
| v/d/j_mismatch_aa | Number of mismatches in the V/D/J region. |
| fwr1/2/3/4_mismatch_aa | Number of mismatches in the FWR1/2/3/4 regions. |
| cdr1/2/3_mismatch_aa | Number of mismatches in the CDR1/2/3 regions. |
- Chart: Statistical analysis results of all input sequences, including the following charts:
- V/D/J gene count histogram.
- VDJ gene combination analyses Sankey diagram.
- CDR1/2/3 Amino Acid Frequency Logo.
Figure 2. V/D/J gene count histogram.
Figure 2. VDJ gene combination analyses Sankey diagram.
Figure 3. V-identity and SHM(aa) histogram.
- Alignment: Detailed information of a single sequence, including a visual alignment chart with homologous sequences, supports PDF format download.
Figure 1. Detailed alignment information and visualization of a single sequence aligned with VDJ genes.
4 Reference
[1] Jian Ye, Ning Ma, Thomas L. Madden, James M. Ostell, IgBLAST: an immunoglobulin variable domain sequence analysis tool, Nucleic Acids Research, Volume 41, Issue W1, 1 July 2013, Pages W34–W40. https://doi.org/10.1093/nar/gkt382