VBASE2
Names
More detailed information about this field from each metasource.
VBASE2
metasource: Fairsharing.org
version: FAIRsharing.org: VBASE2; VBASE2; DOI: https://doi.org/10.25504/FAIRsharing.qvxhb1; Last edited: April 26, 2021, 3:38 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
germ-line V genes
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:12.762833
germ-line_v_genes
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:12.762833
Names
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VBASE2
metasource: Fairsharing.orgversion: FAIRsharing.org: VBASE2; VBASE2; DOI: https://doi.org/10.25504/FAIRsharing.qvxhb1; Last edited: April 26, 2021, 3:38 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
germ-line V genes
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:12.762833
germ-line_v_genes
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:12.762833
Other names: germ-line V genes, germ-line_v_genes
Names
More detailed information about this field from each metasource.
VBASE2
metasource: Fairsharing.orgversion: FAIRsharing.org: VBASE2; VBASE2; DOI: https://doi.org/10.25504/FAIRsharing.qvxhb1; Last edited: April 26, 2021, 3:38 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
germ-line V genes
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:12.762833
germ-line_v_genes
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:12.762833
VBASE2 is an integrative database of germ-line variable genes from the immunoglobulin loci of human and mouse. All variable gene sequences are extracted from the EMBL-Bank.
Description
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VBASE2 is an integrative database of germ-line variable genes from the immunoglobulin loci of human and mouse. All variable gene sequences are extracted from the EMBL-Bank.
metasource: Fairsharing.orgversion: FAIRsharing.org: VBASE2; VBASE2; DOI: https://doi.org/10.25504/FAIRsharing.qvxhb1; Last edited: April 26, 2021, 3:38 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
VBASE2 is an integrative database of germ-line V genes from the immunoglobulin loci of human and mouse. It presents V gene sequences from the EMBL database and Ensembl together with the corresponding links to the source data. The VBASE2 dataset is generated in an automatic process based on a BLAST search of V genes against EMBL and the Ensembl dataset. The BLAST hits are evaluated with the DNAPLOT program, which allows immunoglobulin sequence alignment and comparison, RSS recognition and analysis of the V(D)J-rearrangements. As a result of the BLAST hit evaluation the VBASE2 entries are classified into 3 different classes: class 1 holds sequences for which a genomic reference and a rearranged sequence is known. Class 2 contains sequences which have not been found in a rearrangement, thus lacking evidence of functionality. Class 3 contains sequences which have been found in different V(D)J rearrangements but lack a genomic reference. All VBASE2 sequences are compared with the datasets from the VBASE-, IMGT- and KABAT-databases (latest published versions), and the respective references are provided in each VBASE2 sequence entry. The VBASE2 database can be accessed by either a text based query form or by a sequence alignment with the DNAPLOT program. A DAS-server shows the VBASE2 dataset within the Ensembl Genome Browser and links to the database.
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
An integrative database of germ-line variable genes from the immunoglobulin loci of human and mouse. All variable gene sequences are extracted from the EMBL-Bank.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:12.762833
Webpage:
http://www.vbase2.orgWebpage
More detailed information about this field from each metasource.
http://www.vbase2.org
metasource: Fairsharing.orgversion: FAIRsharing.org: VBASE2; VBASE2; DOI: https://doi.org/10.25504/FAIRsharing.qvxhb1; Last edited: April 26, 2021, 3:38 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
http://www.vbase2.org/
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:12.762833
Licence:
Name: Open Data Commons (ODC) Public Domain Dedication and Licence (PDDL) 1.0Licence name
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Open Data Commons (ODC) Public Domain Dedication and Licence (PDDL) 1.0
metasource: Fairsharing.orgversion: FAIRsharing.org: VBASE2; VBASE2; DOI: https://doi.org/10.25504/FAIRsharing.qvxhb1; Last edited: April 26, 2021, 3:38 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Licence URL
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http://opendatacommons.org/licenses/pddl/1.0/
metasource: Fairsharing.orgversion: FAIRsharing.org: VBASE2; VBASE2; DOI: https://doi.org/10.25504/FAIRsharing.qvxhb1; Last edited: April 26, 2021, 3:38 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Publications:
Publications
More detailed information about this field from each metasource.
VBASE2, an integrative V gene database
PMID: 15608286
metasource: Fairsharing.org
version: FAIRsharing.org: VBASE2; VBASE2; DOI: https://doi.org/10.25504/FAIRsharing.qvxhb1; Last edited: April 26, 2021, 3:38 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
http://dx.doi.org/10.1093/nar/gki088
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:12.762833
Publications
More detailed information about this field from each metasource.
VBASE2, an integrative V gene database
PMID: 15608286
metasource: Fairsharing.org
version: FAIRsharing.org: VBASE2; VBASE2; DOI: https://doi.org/10.25504/FAIRsharing.qvxhb1; Last edited: April 26, 2021, 3:38 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
http://dx.doi.org/10.1093/nar/gki088
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:12.762833
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VBASE2, an integrative V gene database
PubMed citations: 86.
86 articles citing: VBASE2, an integrative V gene database
A BALB/c IGHV Reference Set, Defined by Haplotype Analysis of Long-Read VDJ-C Sequences From F1 (BALB/c x C57BL/6) Mice. PMID:35720344
Analysis of the complete lambda light chain germline usage in patients with AL amyloidosis and dominant heart or kidney involvement. PMID:35213605
Humanization of Camelid Single-Domain Antibodies. PMID:35157279
Follicular T cells optimize the germinal center response to SARS-CoV-2 protein vaccination in mice. PMID:35139367
Novel Allele Detection Tool Benchmark and Application With Antibody Repertoire Sequencing Dataset. PMID:34764956
Human Transbodies to Reverse Transcriptase Connection Subdomain of HIV-1 Gag-Pol Polyprotein Reduce Infectiousness of the Virus Progeny. PMID:34452018
Anti-Idiotype scFv Localizes an Autoepitope in the Globular Domain of C1q. PMID:34361054
The immunodominant antibody response to Zika virus NS1 protein is characterized by cross-reactivity to self. PMID:34292314
Population matched (pm) germline allelic variants of immunoglobulin (IG) loci: Relevance in infectious diseases and vaccination studies in human populations. PMID:34120151
Cryo-EM reveals structural breaks in a patient-derived amyloid fibril from systemic AL amyloidosis. PMID:33558536
Broad specificity of immune helminth scFv library to identify monoclonal antibodies targeting Strongyloides. PMID:33510342
Tunable dynamics of B cell selection in gut germinal centres. PMID:33116306
Computational Model Reveals a Stochastic Mechanism behind Germinal Center Clonal Bursts. PMID:32532145
Restriction of memory B cell differentiation at the germinal center B cell positive selection stage. PMID:32407433
Murine gammaherpesvirus infection is skewed toward Igλ+ B cells expressing a specific heavy chain V-segment. PMID:32353066
A recombinant antibody toolbox for Dictyostelium discoideum. PMID:32276653
A Proposed New Nomenclature for the Immunoglobulin Genes of Mus musculus. PMID:31921202
Restricted Clonality and Limited Germinal Center Reentry Characterize Memory B Cell Reactivation by Boosting. PMID:31866068
Upregulation of tropomyosin alpha-4 chain in patients' saliva with oral squamous cell carcinoma as demonstrated by Phage display. PMID:31804537
Tailoring subtractive cell biopanning to identify diffuse gastric adenocarcinoma-associated antigens via human scFv antibodies. PMID:31596953
Encoding the Sequence of Specific Autoantibodies Against beta-Amyloid and alpha-Synuclein in Neurodegenerative Diseases. PMID:31507618
The ABCD database: a repository for chemically defined antibodies. PMID:31410491
Class-Switch Recombination Occurs Infrequently in Germinal Centers. PMID:31375460
Human antibody repertoire frequently includes antibodies to a bacterial biofilm associated protein. PMID:31287831
Leishmania infantum β-Tubulin Identified by Reverse Engineering Technology through Phage Display Applied as Theranostic Marker for Human Visceral Leishmaniasis. PMID:31013713
Inferred Allelic Variants of Immunoglobulin Receptor Genes: A System for Their Evaluation, Documentation, and Naming. PMID:30936866
Cryo-EM structure of a light chain-derived amyloid fibril from a patient with systemic AL amyloidosis. PMID:30894526
The CDR1 and Other Regions of Immunoglobulin Light Chains are Hot Spots for Amyloid Aggregation. PMID:30816248
A Glucuronoxylomannan Epitope Exhibits Serotype-Specific Accessibility and Redistributes towards the Capsule Surface during Titanization of the Fungal Pathogen Cryptococcus neoformans. PMID:30670549
Phage antibody library screening for the selection of novel high-affinity human single-chain variable fragment against gastrin receptor: an in silico and in vitro study. PMID:30607886
Expression of combinatorial immunoglobulins in macrophages in the tumor microenvironment. PMID:30240437
AbDb: antibody structure database-a database of PDB-derived antibody structures. PMID:29718130
Human transbodies that interfere with the functions of Ebola virus VP35 protein in genome replication and transcription and innate immune antagonism. PMID:29568066
The invasin D protein from Yersinia pseudotuberculosis selectively binds the Fab region of host antibodies and affects colonization of the intestine. PMID:29535184
On being the right size: antibody repertoire formation in the mouse and human. PMID:29260260
Antibody-Based Protective Immunity against Helminth Infections: Antibody Phage Display Derived Antibodies against BmR1 Antigen. PMID:29165352
Reproducibility and Reuse of Adaptive Immune Receptor Repertoire Data. PMID:29163494
Development of unique cytotoxic chimeric antigen receptors based on human scFv targeting B7H6. PMID:29040754
Single amino acid substitution in LC-CDR1 induces Russell body phenotype that attenuates cellular protein synthesis through eIF2α phosphorylation and thereby downregulates IgG secretion despite operational secretory pathway traffic. PMID:28379093
Complement Regulator FHR-3 Is Elevated either Locally or Systemically in a Selection of Autoimmune Diseases. PMID:27965669
Molecular Characterization of Two Monoclonal Antibodies against the Same Epitope on B-Cell Receptor Associated Protein 31. PMID:27907150
Early generated B1 B cells with restricted BCRs become chronic lymphocytic leukemia with continued c-Myc and low Bmf expression. PMID:27899442
Development of a Bioinformatics Framework for the Detection of Gene Conversion and the Analysis of Combinatorial Diversity in Immunoglobulin Heavy Chains in Four Cattle Breeds. PMID:27828971
AIRE-Deficient Patients Harbor Unique High-Affinity Disease-Ameliorating Autoantibodies. PMID:27426947
Determinants of VH1-46 Cross-Reactivity to Pemphigus Vulgaris Autoantigen Desmoglein 3 and Rotavirus Antigen VP6. PMID:27402694
Computationally driven antibody engineering enables simultaneous humanization and thermostabilization. PMID:27334453
Length-independent structural similarities enrich the antibody CDR canonical class model. PMID:26963563
Visualizing antibody affinity maturation in germinal centers. PMID:26912368
The Diversity and Molecular Evolution of B-Cell Receptors during Infection. PMID:26802217
Understanding differences between synthetic and natural antibodies can help improve antibody engineering. PMID:26652053
Antibody humanization by structure-based computational protein design. PMID:26252731
The mouse antibody heavy chain repertoire is germline-focused and highly variable between inbred strains. PMID:26194750
Del(20q) in patients with chronic lymphocytic leukemia: a therapy-related abnormality involving lymphoid or myeloid cells. PMID:25953391
Automated analysis of high-throughput B-cell sequencing data reveals a high frequency of novel immunoglobulin V gene segment alleles. PMID:25675496
Fast track antibody V-gene rescue, recombinant expression in plants and characterization of a PfMSP4-specific antibody. PMID:25651860
Russell body phenotype is preferentially induced by IgG mAb clones with high intrinsic condensation propensity: relations between the biosynthetic events in the ER and solution behaviors in vitro. PMID:25484054
Characterizing immune repertoires by high throughput sequencing: strategies and applications. PMID:25306219
Comparative study of IgA VH 3 gene usage in healthy TST(-) and TST(+) population exposed to tuberculosis: deep sequencing analysis. PMID:25158076
Production and characterization of specific monoclonal antibodies binding the Plasmodium falciparum diagnostic biomarker, histidine-rich protein 2. PMID:25037150
Novel human recombinant antibodies against Mycobacterium tuberculosis antigen 85B. PMID:25033887
A putative OTU domain-containing protein 1 deubiquitinating enzyme is differentially expressed in thyroid cancer and identifies less-aggressive tumours. PMID:24937664
Functional characterization of two scFv-Fc antibodies from an HIV controller selected on soluble HIV-1 Env complexes: a neutralizing V3- and a trimer-specific gp41 antibody. PMID:24828352
A novel antibody against human properdin inhibits the alternative complement system and specifically detects properdin from blood samples. PMID:24797388
Generation of “LYmph Node Derived Antibody Libraries” (LYNDAL) for selecting fully human antibody fragments with therapeutic potential. PMID:24256717
SAbDab: the structural antibody database. PMID:24214988
CARbodies: Human Antibodies Against Cell Surface Tumor Antigens Selected From Repertoires Displayed on T Cell Chimeric Antigen Receptors. PMID:23695536
IgBLAST: an immunoglobulin variable domain sequence analysis tool. PMID:23671333
A fully synthetic human Fab antibody library based on fixed VH/VL framework pairings with favorable biophysical properties. PMID:23571156
An efficient method for variable region assembly in the construction of scFv phage display libraries using independent strand amplification. PMID:22692130
Computer-aided antibody design. PMID:22661385
Immunoglobulin class switching appears to be regulated by B-cell antigen receptor-specific T-cell action. PMID:22531925
A two-gene signature, SKI and SLAMF1, predicts time-to-treatment in previously untreated patients with chronic lymphocytic leukemia. PMID:22194822
Construction and characterization of single-chain variable fragment antibody library derived from germline rearranged immunoglobulin variable genes. PMID:22096568
A database of immunoglobulins with integrated tools: DIGIT. PMID:22080506
Detecting selection in immunoglobulin sequences. PMID:21665923
Utility of Doppler myocardial imaging, cardiac biomarkers, and clonal immunoglobulin genes to assess left ventricular performance and stratify risk following peripheral blood stem cell transplantation in patients with systemic light chain amyloidosis (Al). PMID:21315556
LDOC1 mRNA is differentially expressed in chronic lymphocytic leukemia and predicts overall survival in untreated patients. PMID:21310924
The multicompartmental p32/gClqR as a new target for antibody-based tumor targeting strategies. PMID:21156793
Characterization of gene use and efficacy of mouse monoclonal antibodies to Streptococcus pneumoniae serotype 8. PMID:21068211
Individual variation in the germline Ig gene repertoire inferred from variable region gene rearrangements. PMID:20495067
A humanized anti-VEGF rabbit monoclonal antibody inhibits angiogenesis and blocks tumor growth in xenograft models. PMID:20140208
Identification of a putative Crf splice variant and generation of recombinant antibodies for the specific detection of Aspergillus fumigatus. PMID:19675673
Efficacy of opsonic and nonopsonic serotype 3 pneumococcal capsular polysaccharide-specific monoclonal antibodies against intranasal challenge with Streptococcus pneumoniae in mice. PMID:19168739
Quinine-dependent, platelet-reactive monoclonals mimic antibodies found in patients with quinine-induced immune thrombocytopenia. PMID:18948570
Development of human antibody fragments using antibody phage display for the detection and diagnosis of Venezuelan equine encephalitis virus (VEEV). PMID:18764933
Sequence and characterization of the Ig heavy chain constant and partial variable region of the mouse strain 129S1. PMID:17675503 - http://dx.doi.org/10.1093/nar/gki088
Tags:
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gene
metasource: Fairsharing.org
version: FAIRsharing.org: VBASE2; VBASE2; DOI: https://doi.org/10.25504/FAIRsharing.qvxhb1; Last edited: April 26, 2021, 3:38 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
immunoglobulin complex
metasource: Fairsharing.org
version: FAIRsharing.org: VBASE2; VBASE2; DOI: https://doi.org/10.25504/FAIRsharing.qvxhb1; Last edited: April 26, 2021, 3:38 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
immunological databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
model organisms
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:12.762833
human biology
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:12.762833
immunoproteins and antigens
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:12.762833
Tags
More detailed information about this field from each metasource.
gene
metasource: Fairsharing.orgversion: FAIRsharing.org: VBASE2; VBASE2; DOI: https://doi.org/10.25504/FAIRsharing.qvxhb1; Last edited: April 26, 2021, 3:38 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
immunoglobulin complex
metasource: Fairsharing.orgversion: FAIRsharing.org: VBASE2; VBASE2; DOI: https://doi.org/10.25504/FAIRsharing.qvxhb1; Last edited: April 26, 2021, 3:38 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
immunological databases
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
model organisms
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:12.762833
human biology
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:12.762833
immunoproteins and antigens
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:12.762833
gene immunoglobulin complex immunology model organisms human immunoproteins and antigens
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