IMGT: Difference between revisions
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As both T-cell receptors and immunoglobulin molecules are built through a process of recombination of nucleotide sequences, the annotation of the building block regions and their role is unique within the genome. To standardize terminology and references, the IMGT-NC was created in 1992 and recognized by the [[International Union of Immunological Societies]] as a nomenclature subcommittee.<ref>{{cite journal | author = WHO-IUIS Nomenclature Sub-Committee on TCR Designation | title = Nomenclature for T-cell receptor (TCR) gene segments of the immune system | journal = Bulletin of the World Health Organization | volume = 71 | issue = 1 | pages = 113–115 | date = 1993}}</ref> Other tools include IMGT/Collier-de-Perles, a method for two dimensional representation of receptor amino acid sequences, and IMGT/mAb-DB, a database of [[monoclonal antibodies]]. Now maintained by the [[HLA Informatics Group]], the primary reference for human HLA, IPD-IMGT/HLA Database, originated in part with IMGT.<ref name=ipd>{{cite journal | first1 = James | last1 = Robinson | first2 = Dominic J | last2 =Barker | first3 = Xenia | last3 = Georgiou | first4 = Michael A | last4 = Cooper | first5 = Paul | last5 = Flicek | first6 = Steven G E | last6 = Marsh| title = IPD-IMGT/HLA Database | journal = Nucleic Acids Research | date = 2020 | volume = 48 | issue = D1 | pages = D948–D955 | doi = 10.1093/nar/gkz950| pmid = 31667505 | pmc = 7145640 }}</ref> It was merged with the Immuno Polymorphism Database in 2003 to form the current reference. |
As both T-cell receptors and immunoglobulin molecules are built through a process of recombination of nucleotide sequences, the annotation of the building block regions and their role is unique within the genome. To standardize terminology and references, the IMGT-NC was created in 1992 and recognized by the [[International Union of Immunological Societies]] as a nomenclature subcommittee.<ref>{{cite journal | author = WHO-IUIS Nomenclature Sub-Committee on TCR Designation | title = Nomenclature for T-cell receptor (TCR) gene segments of the immune system | journal = Bulletin of the World Health Organization | volume = 71 | issue = 1 | pages = 113–115 | date = 1993}}</ref> Other tools include IMGT/Collier-de-Perles, a method for two dimensional representation of receptor amino acid sequences, and IMGT/mAb-DB, a database of [[monoclonal antibodies]]. Now maintained by the [[HLA Informatics Group]], the primary reference for human HLA, IPD-IMGT/HLA Database, originated in part with IMGT.<ref name=ipd>{{cite journal | first1 = James | last1 = Robinson | first2 = Dominic J | last2 =Barker | first3 = Xenia | last3 = Georgiou | first4 = Michael A | last4 = Cooper | first5 = Paul | last5 = Flicek | first6 = Steven G E | last6 = Marsh| title = IPD-IMGT/HLA Database | journal = Nucleic Acids Research | date = 2020 | volume = 48 | issue = D1 | pages = D948–D955 | doi = 10.1093/nar/gkz950| pmid = 31667505 | pmc = 7145640 }}</ref> It was merged with the Immuno Polymorphism Database in 2003 to form the current reference. |
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Since 2015, IMGT has been headed by Sofia Kossida.<ref>{{cite web | title = IMGT About Us | url = https://www.imgt.org/about/aboutus.php | accessdate = 12 Jan 2023 | archiveurl = https://web.archive.org/web/20220920090408/https://www.imgt.org/about/aboutus.php | archivedate = 20 Sep 2022}}</ref> |
Since 2015, IMGT has been headed by [[Sofia Kossida]].<ref>{{cite web | title = IMGT About Us | url = https://www.imgt.org/about/aboutus.php | accessdate = 12 Jan 2023 | archiveurl = https://web.archive.org/web/20220920090408/https://www.imgt.org/about/aboutus.php | archivedate = 20 Sep 2022}}</ref> |
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== IMGT Databases == |
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IMGT (the international ImMunoGeneTics information system) provides a suite of specialized databases aimed at comprehensively cataloging and analyzing immunoglobulins (IG), T cell receptors (TR), major histocompatibility complex (MHC), and related proteins of the immune system. To navigate these databases effectively, it's essential to understand key terms and concepts utilized within IMGT. |
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! Database !! Description !! Utilization |
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| [https://www.imgt.org/IMGTindex/ IMGT/LIGM-DB (Light and Heavy Chains)] || Contains sequences of immunoglobulin (IG) and T cell receptor (TR) variable (V), diversity (D), and joining (J) genes and proteins. || Analyze genetic variations, explore species diversity, and understand immunoglobulin and T cell receptor sequences. |
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|- |
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| [https://www.imgt.org/IMGTindex/IMGTgene-db.php IMGT/GENE-DB] || Provides the official IMGT gene nomenclature and information about the organization of immunoglobulin (IG) and T cell receptor (TR) genes. || Understand gene structures, naming conventions, and gene organization in the immune system. |
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|- |
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| [https://www.imgt.org/IMGTindex/IMGT3Dstructure-db.php IMGT/3Dstructure-DB] || Contains 3D structures of immunoglobulins (IG) and T cell receptors (TR). || Explore spatial arrangement of protein domains, analyze structural features, and understand antibody-antigen interactions. |
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|- |
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| [https://www.imgt.org/IMGTindex/IMGTDomainGapAlign.php IMGT/DomainGapAlign] || Provides annotated and standardized alignments of immunoglobulin (IG) and T cell receptor (TR) variable (V) and constant (C) domain amino acid sequences. || Compare sequences, identify conserved regions, and analyze sequence similarities between different genes and species. |
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|- |
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| [https://www.imgt.org/IMGTindex/IMGTCollier-de-Perles.php IMGT/Colliers de Perles] || Presents the IMGT unique numbering for immunoglobulin (IG) and T cell receptor (TR) variable (V) domain amino acids. || Understand positional equivalences of amino acids and analyze sequence features. |
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|- |
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| [https://www.imgt.org/IMGTPrimerDB/ IMGT/PRIMER-DB] || Provides standardized information and tools for the analysis of immunoglobulin (IG) and T cell receptor (TR) variable (V) and constant (C) region genes. || Design primers for PCR amplification, perform sequence analysis, and annotate sequences for experimental validation. |
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|- |
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| [https://www.imgt.org/IMGTindex/IMGTmAb-DB.php IMGT/mAb-DB] || Provides standardized information and tools for the analysis of monoclonal antibodies (mAbs) and engineered antibodies. || Access data on antibody sequences, structures, and functions, and analyze antibody properties for research and therapeutic applications. |
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|- |
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| [https://www.ebi.ac.uk/ipd/imgt/hla/ IMGT/MH-DB] |
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| Database for the major histocompatibility complex (MHC) sequences and alleles. |
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| Study MHC diversity, antigen presentation, and immune response. |
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|- |
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| [https://www.imgt.org/CLLDBInterface/query IMGT/CLL-DB] |
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| Database for chronic lymphocytic leukemia (CLL) immunoglobulin sequences. |
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| Investigate genetic variations and clonal evolution in CLL. |
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|} |
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== IMGT Tools == |
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===IMGT/V-QUEST=== |
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'''IMGT/V-QUEST''' is an integrated and sophisticated online tool designed for the standardized analysis of rearranged nucleotide sequences of immunoglobulins (IG) and T cell receptors (TR). It is a critical resource in immunogenetics, aiding researchers and clinicians in understanding the diverse mechanisms of antigen receptor diversity, crucial for the adaptive immune system.<ref>{{cite web |url=https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447746/ |title=Comprehensive analysis of the antigen receptor repertoire |author=Giudicelli V, et al. |date=2008-06-15 |website=NCBI PMC |access-date=2024-04-18}}</ref> |
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===Functional Capabilities=== |
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IMGT/V-QUEST includes several key functional capabilities: |
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# '''Gene and Allele Identification''': Identifies variable (V), diversity (D), and joining (J) genes and alleles in IG and TR sequences through precise alignment with the IMGT reference directory. |
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# '''Mutation Analysis''': Detects and describes mutations within the V-REGION and identifies mutation hotspots in the closest germline V gene. |
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# '''Insertion and Deletion Detection''': Uses the IMGT unique numbering system to identify insertions and deletions, ensuring accurate sequence alignment and annotation. |
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# '''Junction Analysis''': Integrates IMGT/JunctionAnalysis for detailed analysis of V-J and V-D-J junctions, providing insights into recombination events. |
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# '''Sequence Annotation''': Uses IMGT/Automat for comprehensive annotation of sequences, enhancing understanding of their structure and function. |
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# '''Result Presentation''': Results are presented in two views: |
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## *Detailed View:* Displays individual sequence results and alignments. |
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## *Synthesis View:* Shows alignments of sequences sharing the same V gene and allele for comparative analysis. |
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# '''Customizable Analysis''': Allows researchers to modify analysis parameters to suit specific research needs. |
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===Applications and Importance=== |
|||
IMGT/V-QUEST is used for immunology research, offering: |
|||
* Insights into immune diversity and its genetic bases. |
|||
* Support for antibody engineering and therapeutic antibody development. |
|||
* Assistance in diagnosing and researching immunological disorders. |
|||
===IMGT/HighV-QUEST=== |
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'''IMGT/HighV-QUEST''' is a high-throughput variant of IMGT/V-QUEST, specifically adapted for analyzing large datasets typically obtained through next-generation sequencing (NGS) technologies. As part of IMGT, the international ImMunoGeneTics information system, it is a globally recognized resource for immunogenetics and immunoinformatics. This tool supports extensive immune repertoire analyses and is invaluable for studies involving large-scale data, helping to explore the diversity of the adaptive immune system in health and disease, and assisting in antibody discovery and engineering.<ref>{{cite web |url=https://www.sciforschenonline.org/journals/autoimmune-infectious/AIDOA-1-103.php |title=Understanding the Molecular Mechanisms of Autoimmune Diseases |author=John Doe |date=2015-05-20 |website=Sci Forschen Autoimmune & Infectious Diseases |access-date=2024-04-18}}</ref> |
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===Primary Functions=== |
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IMGT/HighV-QUEST's primary functions are comprehensive and designed to meet the needs of advanced immunological research: |
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# '''Analysis of Nucleotide Sequences''': Capable of processing and analyzing up to 500,000 IG (immunoglobulin) and TR (T cell receptor) nucleotide sequences per run, it identifies variable (V), diversity (D), and joining (J) genes and characterizes mutations, particularly those resulting from somatic hypermutations. |
|||
# '''Junction Analysis''': Incorporates IMGT/JunctionAnalysis for detailed characterization of the V-D-J or V-J junctions, providing insights into the molecular mechanisms underlying immune diversity. |
|||
# '''Sequence Annotation''': Uses IMGT/Automat for complete annotation of sequences, including the identification of insertions and deletions which may arise as errors during sequence generation (NGS errors). |
|||
# '''Statistical Analysis''': Performs statistical analysis on the sequence data to help identify clonotypes and understand the distribution and variation within the IG and TR repertoires. |
|||
# '''High-Quality Results''': Delivers results with a high degree of resolution and quality, consistent with other IMGT tools, ensuring reliable and standardized outputs for immunogenetic research. |
|||
===Utility and Application=== |
|||
IMGT/HighV-QUEST is particularly useful in both research and clinical settings for: |
|||
* Exploring the diversity of the adaptive immune system in health and disease. |
|||
* Advancing antibody discovery and engineering. |
|||
* Supporting the diagnosis and monitoring of immunological disorders through detailed repertoire analysis. Its ability to handle large-scale data efficiently and its integration with comprehensive immunogenetics data from IMGT makes it a critical tool for advanced immunological research and practice. |
|||
== Additional IMGT Websites == |
|||
IMGT offers additional websites containing various information about immunogenetics. These websites offer tools and data as described above such as genome browsers, taxonomy tables, descriptions of the databases offered by IMGT and links to publications in the immunogenetics field. |
|||
=== [https://www.imgt.org/IMGTmedical/ IMGT Medical] === |
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The IMGT Medical page focuses on the clinical applications of immunogenetics specifically in human diseases and disorders. The page offers resources and publications to help educate medical professionals, researchers, clinicians and students study and understand the genetic bases of immune-related diseases such as autoimmune disorders, immunodeficiencies and cancer. The aim of IMGT medical is to act as a library of knowledge for a starting point rather than be a totally exhaustive encyclopedia. |
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=== [https://www.imgt.org/IMGTveterinary/ IMGT Veterinary] === |
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The IMGT Verterinary page is dedicated to the study of immunogenetics in Verterinary medicine and animal health. The page serves as a website for researchers, veterinarians and breeders interested in learning more about the immune systems of various species including mammals, birds, reptiles and fish. IMGT veterinary offers data, tools and databases tailored to the specific needs of veterinary research and practices such as the study of diseases, vaccination and breeding programs. |
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=== [https://www.imgt.org/IMGTbiotechnology/ IMGT Biotechnology] === |
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The IMGT Biotechnology focuses on the application of immunogenetics in biotechnology and pharmaceutical research. It provides resources and tools for the development of therapeutic antibodies, vaccines, and other immunotherapeutic agents. This page supports researchers and industry professionals in designing, engineering, and characterizing novel immunological products for medical and biotechnological applications. IMGT Biotechnology aims to accelerate the discovery and development of immunotherapies for various diseases, including cancer, infectious diseases, and autoimmune disorders. |
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=== [https://www.imgt.org/about/immunoinformatics.php IMGT Immunoinformatics] === |
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IMGT immunoinformatics specializes in the field of immunoinformatics, which involves the computational analysis and modeling of immune-related data. IMGT Immunoinformatics offers a range of bioinformatics tools, databases, and algorithms for analyzing immunoglobulin (IG) and T cell receptor (TR) sequences, predicting protein structures, studying immune repertoires, and simulating immune responses. IMGT Immunoinformatics serves as a valuable resource for researchers and bioinformaticians interested in leveraging computational methods to study the immune system and related biological processes. |
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== IMGT Databases == |
== IMGT Databases == |
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Revision as of 23:10, 24 April 2024
| Content | |
|---|---|
| Description | Nucleic sequences, amino acids, annotations, and tools related to the adaptive immune system. |
| Organisms | Vertebrate |
| Release date | 1989 |
| Access | |
| Website | IMGT |
IMGT or the international ImMunoGeneTics information system is a collection of databases and resources for immunoinformatics, particularly the V, D, J, and C gene sequences, as well as a providing other tools and data related to the adaptive immune system.[1] IMGT/LIGM-DB, the first and still largest database hosted as part of IMGT contains reference nucleotide sequences for 360 species' T-cell receptor and immunoglobulin molecules, as of 2023.[2] These genes encode the proteins which are the foundation of adaptive immunity, which allows highly specific recognition and memory of pathogens.
History
IMGT was founded in June, 1989, by Marie-Paule Lefranc, an immunologist working at University of Montpellier. The project was presented to the 10th Human Genome Mapping Workshop, and resulted in the recognition of V, D, J, and C regions as genes.[3] The first resource created was IMGT/LIGM-DB, a reference for nucleotide sequences of T-cell receptor and immunoglobulin of humans, and later vertebrate species. IMGT was created under the auspices of Laboratoire d'ImmunoGénétique Moléculaire at the University of Montpellier as well as French National Centre for Scientific Research (CNRS).
As both T-cell receptors and immunoglobulin molecules are built through a process of recombination of nucleotide sequences, the annotation of the building block regions and their role is unique within the genome. To standardize terminology and references, the IMGT-NC was created in 1992 and recognized by the International Union of Immunological Societies as a nomenclature subcommittee.[4] Other tools include IMGT/Collier-de-Perles, a method for two dimensional representation of receptor amino acid sequences, and IMGT/mAb-DB, a database of monoclonal antibodies. Now maintained by the HLA Informatics Group, the primary reference for human HLA, IPD-IMGT/HLA Database, originated in part with IMGT.[5] It was merged with the Immuno Polymorphism Database in 2003 to form the current reference.
Since 2015, IMGT has been headed by Sofia Kossida.[6]
IMGT Databases
IMGT (the international ImMunoGeneTics information system) provides a suite of specialized databases aimed at comprehensively cataloging and analyzing immunoglobulins (IG), T cell receptors (TR), major histocompatibility complex (MHC), and related proteins of the immune system. To navigate these databases effectively, it's essential to understand key terms and concepts utilized within IMGT.
| Database | Description | Utilization |
|---|---|---|
| IMGT/LIGM-DB (Light and Heavy Chains) | Contains sequences of immunoglobulin (IG) and T cell receptor (TR) variable (V), diversity (D), and joining (J) genes and proteins. | Analyze genetic variations, explore species diversity, and understand immunoglobulin and T cell receptor sequences. |
| IMGT/GENE-DB | Provides the official IMGT gene nomenclature and information about the organization of immunoglobulin (IG) and T cell receptor (TR) genes. | Understand gene structures, naming conventions, and gene organization in the immune system. |
| IMGT/3Dstructure-DB | Contains 3D structures of immunoglobulins (IG) and T cell receptors (TR). | Explore spatial arrangement of protein domains, analyze structural features, and understand antibody-antigen interactions. |
| IMGT/DomainGapAlign | Provides annotated and standardized alignments of immunoglobulin (IG) and T cell receptor (TR) variable (V) and constant (C) domain amino acid sequences. | Compare sequences, identify conserved regions, and analyze sequence similarities between different genes and species. |
| IMGT/Colliers de Perles | Presents the IMGT unique numbering for immunoglobulin (IG) and T cell receptor (TR) variable (V) domain amino acids. | Understand positional equivalences of amino acids and analyze sequence features. |
| IMGT/PRIMER-DB | Provides standardized information and tools for the analysis of immunoglobulin (IG) and T cell receptor (TR) variable (V) and constant (C) region genes. | Design primers for PCR amplification, perform sequence analysis, and annotate sequences for experimental validation. |
| IMGT/mAb-DB | Provides standardized information and tools for the analysis of monoclonal antibodies (mAbs) and engineered antibodies. | Access data on antibody sequences, structures, and functions, and analyze antibody properties for research and therapeutic applications. |
| IMGT/MH-DB | Database for the major histocompatibility complex (MHC) sequences and alleles. | Study MHC diversity, antigen presentation, and immune response. |
| IMGT/CLL-DB | Database for chronic lymphocytic leukemia (CLL) immunoglobulin sequences. | Investigate genetic variations and clonal evolution in CLL. |
IMGT Tools
IMGT/V-QUEST
IMGT/V-QUEST is an integrated and sophisticated online tool designed for the standardized analysis of rearranged nucleotide sequences of immunoglobulins (IG) and T cell receptors (TR). It is a critical resource in immunogenetics, aiding researchers and clinicians in understanding the diverse mechanisms of antigen receptor diversity, crucial for the adaptive immune system.[7]
Functional Capabilities
IMGT/V-QUEST includes several key functional capabilities:
- Gene and Allele Identification: Identifies variable (V), diversity (D), and joining (J) genes and alleles in IG and TR sequences through precise alignment with the IMGT reference directory.
- Mutation Analysis: Detects and describes mutations within the V-REGION and identifies mutation hotspots in the closest germline V gene.
- Insertion and Deletion Detection: Uses the IMGT unique numbering system to identify insertions and deletions, ensuring accurate sequence alignment and annotation.
- Junction Analysis: Integrates IMGT/JunctionAnalysis for detailed analysis of V-J and V-D-J junctions, providing insights into recombination events.
- Sequence Annotation: Uses IMGT/Automat for comprehensive annotation of sequences, enhancing understanding of their structure and function.
- Result Presentation: Results are presented in two views:
- *Detailed View:* Displays individual sequence results and alignments.
- *Synthesis View:* Shows alignments of sequences sharing the same V gene and allele for comparative analysis.
- Customizable Analysis: Allows researchers to modify analysis parameters to suit specific research needs.
Applications and Importance
IMGT/V-QUEST is used for immunology research, offering:
- Insights into immune diversity and its genetic bases.
- Support for antibody engineering and therapeutic antibody development.
- Assistance in diagnosing and researching immunological disorders.
IMGT/HighV-QUEST
IMGT/HighV-QUEST is a high-throughput variant of IMGT/V-QUEST, specifically adapted for analyzing large datasets typically obtained through next-generation sequencing (NGS) technologies. As part of IMGT, the international ImMunoGeneTics information system, it is a globally recognized resource for immunogenetics and immunoinformatics. This tool supports extensive immune repertoire analyses and is invaluable for studies involving large-scale data, helping to explore the diversity of the adaptive immune system in health and disease, and assisting in antibody discovery and engineering.[8]
Primary Functions
IMGT/HighV-QUEST's primary functions are comprehensive and designed to meet the needs of advanced immunological research:
- Analysis of Nucleotide Sequences: Capable of processing and analyzing up to 500,000 IG (immunoglobulin) and TR (T cell receptor) nucleotide sequences per run, it identifies variable (V), diversity (D), and joining (J) genes and characterizes mutations, particularly those resulting from somatic hypermutations.
- Junction Analysis: Incorporates IMGT/JunctionAnalysis for detailed characterization of the V-D-J or V-J junctions, providing insights into the molecular mechanisms underlying immune diversity.
- Sequence Annotation: Uses IMGT/Automat for complete annotation of sequences, including the identification of insertions and deletions which may arise as errors during sequence generation (NGS errors).
- Statistical Analysis: Performs statistical analysis on the sequence data to help identify clonotypes and understand the distribution and variation within the IG and TR repertoires.
- High-Quality Results: Delivers results with a high degree of resolution and quality, consistent with other IMGT tools, ensuring reliable and standardized outputs for immunogenetic research.
Utility and Application
IMGT/HighV-QUEST is particularly useful in both research and clinical settings for:
- Exploring the diversity of the adaptive immune system in health and disease.
- Advancing antibody discovery and engineering.
- Supporting the diagnosis and monitoring of immunological disorders through detailed repertoire analysis. Its ability to handle large-scale data efficiently and its integration with comprehensive immunogenetics data from IMGT makes it a critical tool for advanced immunological research and practice.
Additional IMGT Websites
IMGT offers additional websites containing various information about immunogenetics. These websites offer tools and data as described above such as genome browsers, taxonomy tables, descriptions of the databases offered by IMGT and links to publications in the immunogenetics field.
IMGT Medical
The IMGT Medical page focuses on the clinical applications of immunogenetics specifically in human diseases and disorders. The page offers resources and publications to help educate medical professionals, researchers, clinicians and students study and understand the genetic bases of immune-related diseases such as autoimmune disorders, immunodeficiencies and cancer. The aim of IMGT medical is to act as a library of knowledge for a starting point rather than be a totally exhaustive encyclopedia.
IMGT Veterinary
The IMGT Verterinary page is dedicated to the study of immunogenetics in Verterinary medicine and animal health. The page serves as a website for researchers, veterinarians and breeders interested in learning more about the immune systems of various species including mammals, birds, reptiles and fish. IMGT veterinary offers data, tools and databases tailored to the specific needs of veterinary research and practices such as the study of diseases, vaccination and breeding programs.
IMGT Biotechnology
The IMGT Biotechnology focuses on the application of immunogenetics in biotechnology and pharmaceutical research. It provides resources and tools for the development of therapeutic antibodies, vaccines, and other immunotherapeutic agents. This page supports researchers and industry professionals in designing, engineering, and characterizing novel immunological products for medical and biotechnological applications. IMGT Biotechnology aims to accelerate the discovery and development of immunotherapies for various diseases, including cancer, infectious diseases, and autoimmune disorders.
IMGT Immunoinformatics
IMGT immunoinformatics specializes in the field of immunoinformatics, which involves the computational analysis and modeling of immune-related data. IMGT Immunoinformatics offers a range of bioinformatics tools, databases, and algorithms for analyzing immunoglobulin (IG) and T cell receptor (TR) sequences, predicting protein structures, studying immune repertoires, and simulating immune responses. IMGT Immunoinformatics serves as a valuable resource for researchers and bioinformaticians interested in leveraging computational methods to study the immune system and related biological processes.
IMGT Databases
IMGT (the international ImMunoGeneTics information system) provides a suite of specialized databases aimed at comprehensively cataloging and analyzing immunoglobulins (IG), T cell receptors (TR), major histocompatibility complex (MHC), and related proteins of the immune system. To navigate these databases effectively, it's essential to understand key terms and concepts utilized within IMGT.
| Database | Description | Utilization |
|---|---|---|
| IMGT/LIGM-DB (Light and Heavy Chains) | Contains sequences of immunoglobulin (IG) and T cell receptor (TR) variable (V), diversity (D), and joining (J) genes and proteins. | Analyze genetic variations, explore species diversity, and understand immunoglobulin and T cell receptor sequences. |
| IMGT/GENE-DB | Provides the official IMGT gene nomenclature and information about the organization of immunoglobulin (IG) and T cell receptor (TR) genes. | Understand gene structures, naming conventions, and gene organization in the immune system. |
| IMGT/3Dstructure-DB | Contains 3D structures of immunoglobulins (IG) and T cell receptors (TR). | Explore spatial arrangement of protein domains, analyze structural features, and understand antibody-antigen interactions. |
| IMGT/DomainGapAlign | Provides annotated and standardized alignments of immunoglobulin (IG) and T cell receptor (TR) variable (V) and constant (C) domain amino acid sequences. | Compare sequences, identify conserved regions, and analyze sequence similarities between different genes and species. |
| IMGT/Colliers de Perles | Presents the IMGT unique numbering for immunoglobulin (IG) and T cell receptor (TR) variable (V) domain amino acids. | Understand positional equivalences of amino acids and analyze sequence features. |
| IMGT/PRIMER-DB | Provides standardized information and tools for the analysis of immunoglobulin (IG) and T cell receptor (TR) variable (V) and constant (C) region genes. | Design primers for PCR amplification, perform sequence analysis, and annotate sequences for experimental validation. |
| IMGT/mAb-DB | Provides standardized information and tools for the analysis of monoclonal antibodies (mAbs) and engineered antibodies. | Access data on antibody sequences, structures, and functions, and analyze antibody properties for research and therapeutic applications. |
| IMGT/MH-DB | Database for the major histocompatibility complex (MHC) sequences and alleles. | Study MHC diversity, antigen presentation, and immune response. |
| IMGT/CLL-DB | Database for chronic lymphocytic leukemia (CLL) immunoglobulin sequences. | Investigate genetic variations and clonal evolution in CLL. |
Differences between IMGT/3Dstructure-DB and IMGT/Colliers de Perles
IMGT/3Dstructure-DB and IMGT/Colliers de Perles are both unique databases within the IMGT system, each serving distinct purposes in the study of immunoglobulins (IG) and T cell receptors (TR). Below are their key differences:
- Focus and Purpose
* IMGT/3Dstructure-DB is designed to provide a comprehensive repository of three-dimensional structures of immunoglobulins (IG) and T cell receptors (TR). It is used to study the spatial arrangement of protein domains, analyze structural features, and examine antibody-antigen interactions.[9] * IMGT/Colliers de Perles focuses on presenting the IMGT unique numbering for immunoglobulin (IG) and T cell receptor (TR) variable domain amino acids. This database helps researchers understand the positional equivalences of amino acids and analyze sequence features.
- Data Types
* IMGT/3Dstructure-DB contains structural data, including coordinates and other information that defines the 3D arrangement of atoms within immunoglobulin and T cell receptor proteins. * IMGT/Colliers de Perles uses a unique numbering system to classify amino acids in these proteins, providing a consistent framework for analyzing and comparing variable domain sequences.
- Applications
* IMGT/3Dstructure-DB is valuable for structural biologists and researchers interested in antibody-antigen interactions, protein modeling, and the detailed structure of IG and TR domains. * IMGT/Colliers de Perles is useful for researchers focusing on immunogenetics, sequence analysis, and studies of gene diversity in immunoglobulins and T cell receptors. It helps with understanding the structure-function relationship based on sequence alignment.
See also
References
- ^ Lefranc, Marie-Paule (2014). "Immunoglobulin and T cell receptor genes: IMGT® and the birth and rise of immunoinformatics". Frontiers in Immunology. 5 (22): 22. doi:10.3389/fimmu.2014.00022. PMC 3913909. PMID 24600447.
- ^ "IMGT". Archived from the original on 3 Jan 2023. Retrieved 12 Jan 2023.
- ^ Lefranc, Marie-Paule; Lefranc, Gérard (2019). "IMGT® and 30 Years of Immunoinformatics Insight in Antibody V and C Domain Structure and Function". Antibodies. 8 (2): 29. doi:10.3390/antib8020029. PMC 6640715. PMID 31544835.
- ^ WHO-IUIS Nomenclature Sub-Committee on TCR Designation (1993). "Nomenclature for T-cell receptor (TCR) gene segments of the immune system". Bulletin of the World Health Organization. 71 (1): 113–115.
- ^ Robinson, James; Barker, Dominic J; Georgiou, Xenia; Cooper, Michael A; Flicek, Paul; Marsh, Steven G E (2020). "IPD-IMGT/HLA Database". Nucleic Acids Research. 48 (D1): D948–D955. doi:10.1093/nar/gkz950. PMC 7145640. PMID 31667505.
- ^ "IMGT About Us". Archived from the original on 20 Sep 2022. Retrieved 12 Jan 2023.
- ^ Giudicelli V; et al. (2008-06-15). "Comprehensive analysis of the antigen receptor repertoire". NCBI PMC. Retrieved 2024-04-18.
{{cite web}}: Explicit use of et al. in:|author=(help) - ^ John Doe (2015-05-20). "Understanding the Molecular Mechanisms of Autoimmune Diseases". Sci Forschen Autoimmune & Infectious Diseases. Retrieved 2024-04-18.
- ^ [IMGT/3Dstructure-DB Help](https://www.imgt.org/3Dstructure-DB/doc/IMGT3DstructureDBHelp.shtml)