DTU Health Tech

Department of Health Technology

MAIT Match - 1.0

Calculate similarity between CDR3 sequences and a reference database of MAIT sequences


SUBMISSION

Paste a single or several peptides in PEPTIDE format into the field below:

or submit a file in PEPTIDE format directly from your local disk:

Exclude self 

Optional: Paste in a custom-based MAIT reference database (in the following format) into the field below:

or submit a file with a custom-based MAIT reference database (in the following format directly from your local disk:


If nothing is uploaded, the database used is found in the MAIT Database tab.

Restrictions:
At most 5000 sequences per submission; each sequence not more than 20,000 amino acids and not less than 8 amino acids.

Confidentiality:
The sequences are kept confidential and will be deleted after processing.


CITATIONS AND FUNDING

For publication of results, please cite:


PORTABLE VERSION

Would you prefer to run MAIT Match at your own site? Mait_Match v. 1.0 is available as a stand-alone software package, with the same functionality as the service above. Ready-to-ship packages exist for the most common UNIX platforms. There is a download tab for academic users; other users are requested to contact the Software Package Manager at health-software@dtu.dk.

Output format



DESCRIPTION

The prediction output consists of 3 columns (Ignoring the first).

  • Sequence
  • MAIT_hit sequence
  • Score of best MAIT hit The score is calculated by scoring matching the query sequence against the database of MAIT sequences and reporting the best scoring match. Match scores fall between 0 and 1, where 1 is the score for a perfect match.

  • EXAMPLE OUTPUT

    
    
    # Read 21 elements on linelist /home/projects/mniel/MAIT_Match/data/blosum62.qij
    # Number of PEP entries read 10 from file /usr/opt/www/webface/tmp/server/mait_match/5543C1FC0000566C77B8007C/file.0
    # Number of PEP entries read 187 from file /home/projects/mniel/MAIT_Match/data/MAIT_DB_update
    Res              Sequence             MAIT_hit  Score
    Best    CAMRESISSGSARQLTF         CAPSGSARQLTF 0.8331
    Best      CAANVGGGSNYKLTF      CAVPNSGGSNYKLTF 0.8718
    Best        CAGGDNYGQNFVF        CAVQGNYGQNFVF 0.8706
    Best    CAMRESISSGSARQLTF         CAPSGSARQLTF 0.8331
    Best     CALGELWDQAGTALIF        CAVLGQAGTALIF 0.8161
    Best        CAMSEGGYNKLIF         CAVGSGGYNKLI 0.8884
    Best      CAGAPRDNYGQNFVF       CAVEEDNYGQNFVF 0.8308
    Best        CAVEPGGYQKVTF         CVAYSGGYQKVT 0.8595
    Best    CACDPLGGGDTTDKLIF         CAVGEDTGKLIF 0.7544
    Best         CAVNPNDYKLSF         CAVLSNDYKLSF 0.9019
    

    Article abstracts


    Main reference:

    A population of pro-inflammatory TRAV1-2+ CD8+ T-cells including oligoconal expansions of MAIT cells is enriched in the airways in human tuberculosis
    Emily B. Wong 1,2, Marielle C. Gold3,4,5, Umesh Lalloo6, Bongiwe Z. Xulu1, Zuri A. Sullivan1, Zoe Rogers1, Henrik Kloverpris1, Erin W. Meermeier5, Prabhat K. Sharma4, Aneta H. Worley 3,4, Prinita Baijnath6, Anish Ambaram6, Leon Naidoo6, Rajhmun Madansein7, James E. McLaren8, David A. Price 8,9, Samuel M. Behar10, Morten Nielsen11, Victoria O. Kasprowicz1,12,13, Alasdair Leslie1, Thumbi Ndung'u1,12,13,14, William R. Bishai15, David M. Lewinsohn3,4,5.

    Abstract

    Mucosal-associated invariant T (MAIT) cells typically express a TRAV1-2+ semi-invariant TCR that enables recognition of bacterial, mycobacterial, and fungal riboflavin metabolites presented by MR1. MAIT cells are associated with immune control of bacterial and mycobacterial infections in murine models. Here, we report that a population of pro-inflammatory TRAV1-2+ CD8+ T cells are present in the airways and lungs of healthy individuals and are enriched in bronchoalveolar fluid of patients with active pulmonary tuberculosis (TB). High-throughput T cell receptor analysis reveals oligoclonal expansions of canonical and donor-unique TRAV1-2+ MAIT-consistent TCR# sequences within this population. Some of these cells demonstrate MR1-restricted mycobacterial reactivity and phenotypes suggestive of MAIT cell identity. These findings demonstrate enrichment of TRAV1-2+ CD8+ T cells with MAIT or MAIT-like features in the airways during active TB and suggest a role for these cells in the human pulmonary immune response to Mycobacterium tuberculosis. 1KwaZulu-Natal Research Institute for Tuberculosis and HIV, Durban, South Africa
    2Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
    3Department of Pulmonary & Critical Care Medicine, Oregon Health & Science University, Portland, OR, USA
    4 VA Portland Health Care Center, Portland, OR, USA
    5Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, Oregon 97239, USA
    6Department of Pulmonology and Critical Care, Nelson Mandela School of Medicine, University of KwaZulu Natal, Durban, South Africa
    7Department of Cardiothoracic Surgery, Nelson Mandela School of Medicine, University of KwaZulu Natal, Durban, South Africa
    8Institute of Infection & Immunity, Cardiff University School of Medicine, Cardiff, Wales, UK
    9Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
    10Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA
    11Center for Biological Sequence Analysis, BioCentrum-DTU, Technical University of Denmark, Lyngby, Denmark
    12 HIV Pathogenesis Programme, University of KwaZulu-Natal, Durban, South Africa
    13 The Ragon Institute of MGH, MIT, and Harvard, Harvard Medical School, Cambridge, MA
    14Max Planck Institute for Infection Biology, Berlin, Germany
    15Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD

    CAAEDSNYQLIW
    CAAESNSGYALNF
    CAAFDSNYQLIW
    CAAFDSNYRLIF
    CAAGGQNFVF
    CAAIDSNYQLIW
    CAALDSNYQLIW
    CAALNSNYQLIW
    CAALSDYKLSF
    CAALSNDYKLSF
    CAAMDSNYQLIW
    CAANREGAQKLVF
    CAAPTGRRALTF
    CAASAAGYGNKLVF
    CAASDSNYQLIW
    CAASKAAGNKLTF
    CAASKSGYSTLT
    CAASMGYSSASKIIF
    CAATGNQGAQKLVF
    CAAVDSNYQLIW
    CADLSNSGYALNF
    CAEAQGGTALIF
    CAEMEIYNQGGKLIF
    CAETGIHNAGNNRKLIF
    CAFMDSNYQLIW
    CAGERAEYGNKLVF
    CAGGANAGGTSYGKLTF
    CAGGTGTASKLTF
    CAGHDRAGSYQLTF
    CAGLDSNYQLIW
    CAGMDSNYQLIW
    CAGPPNGNKLVF
    CAGWDSNYQLIW
    CAIIGFGGSQGNLI
    CAIMDSNYQLIW
    CAIPQGGSEKLV
    CALDPRVGGFKTIF
    CALGENYLPPTGNTPLV
    CALGHMNRDDKIIF
    CALGRRSSASKIIF
    CALGRWSSASKIIF
    CALLDSNYQLIW
    CALLTNFGNEKLT
    CALNDMRF
    CALRDTGFQKLVF
    CALSEGPLTGNQFY
    CAMREADSSYKLIF
    CAMRERRYSSASKIIF
    CAMRESYGNNRLAF
    CAMSINYGGSQGNLI
    CAPLDSNYQLIW
    CAPMDSNYQLIW
    CAPSGSARQLTF
    CAPVDSSYKLIF
    CARGMDSSYKLIF
    CARGYSGGGADGLT
    CARMDSNYQLIW
    CARSDSNYQLIW
    CASEGCGNKLVF
    CASIDSNYQLIW
    CASLDSSYKLIF
    CASMDSNYQLIW
    CASMDSSYKLIF
    CASRSYNTDKLIF
    CASSDSKYQLIW
    CATMDSNYQLIW
    CAVAGAPGGSYIPTF
    CAVDDNTDKLIF
    CAVEAWNNAGNMLTF
    CAVEDPQTGANNLF
    CAVEEDNYGQNFVF
    CAVEPPIVGKST
    CAVEPRTSGGSYIPTF
    CAVEPWTSGGSYIPTF
    CAVESNSGYALNF
    CAVFSDGQKLLF
    CAVGADDYKLSF
    CAVGDNAGNMLTF
    CAVGDSNYQLIW
    CAVGEDTGKLIF
    CAVGSGGYNKLI
    CAVGYSSASKIIF
    CAVIDSNYQLIW
    CAVIGGFGNVLHC
    CAVIQGDYKLSF
    CAVKDSNYQLIW
    CAVKEGNYQLIW
    CAVLDGNYQLIW
    CAVLDSNYQLIW
    CAVLDSSYKLIF
    CAVLGQAGTALIF
    CAVLNAGGFKTIF
    CAVLNTGGFKTIF
    CAVLQGDYKLSF
    CAVLSNAYKLSF
    CAVLSNDYKLSF
    CAVMDDNYQLIW
    CAVMDSNYQLIW
    CAVMDSSYKLIF
    CAVMGGYNFNKFYF
    CAVMGSSYKLIF
    CAVMRNAGNMLTF
    CAVNNNNDMRF
    CAVPFYSSASKIIF
    CAVPNSGGSNYKLTF
    CAVPNYNQGGKLIF
    CAVPREGVDNTDKLIF
    CAVPSGGSYIPTF
    CAVQDSNYQLIW
    CAVQGNYGQNFVF
    CAVQNSNYQLIW
    CAVRADNNARLMF
    CAVRDGAGIKIIF
    CAVRDGAGNMLTF
    CAVRDGAGNRLTF
    CAVRDGDYKLIF
    CAVRDGDYKLSF
    CAVRDGDYKPSF
    CAVRDGHYKLSF
    CAVRDGNYQLIW
    CAVRDGTDSWGKLQF
    CAVRDNDYKLSF
    CAVRDNFNKFYF
    CAVRDPDNARLMF
    CAVRDRDYKLSF
    CAVRDRDYQLIW
    CAVRDREYGNKLVF
    CAVRDRILNYGGATNKLIF
    CAVRDRLNARLMF
    CAVRDRNYGGATNKLIF
    CAVRDRQAGTALIF
    CAVRDSDYKLSF
    CAVRDSNYQLIW
    CAVRDSSYKLIF
    CAVRDTGFQKLVF
    CAVRDWTGANNLF
    CAVRERGDADNMLTF
    CAVRERGDAGNMLTF
    CAVRERGGAGNMLTF
    CAVRESNYQLIW
    CAVRGATDSWGKLQF
    CAVRGDNYQLIW
    CAVRGGDYKLSF
    CAVRGGWDSNYQLIW
    CAVRGLTYNTDKLIF
    CAVRGNFNKFYF
    CAVRLHDKLIF
    CAVRLHSNYQLIW
    CAVRNSNYQLIW
    CAVRQINTGTASKLTF
    CAVRRDDKIIF
    CAVRRRDDKIIF
    CAVRRYSGAGSYQLTF
    CAVRSEGARLMF
    CAVRVDRGSTLGRLYF
    CAVRVVNNAGNMLTF
    CAVRVVYNQGGKLIF
    CAVSDSNYQLIW
    CAVSDSSYKLIF
    CAVSGDYKLSF
    CAVSPEDSNYQLIW
    CAVTDSNYQLIW
    CAVTPPSGGSYIPTF
    CAVVDSNYQLIW
    CAVVNYGQNFVF
    CAVWYSWGKLQF
    CAVYDSNYQLIW
    CAVYGDMRF
    CAWLRFQKLVF
    CGQEEATYLHLEEGRGSYIPTF
    CILQQDAGGNSYGKLTF
    CIPLDSSNTGKLIF
    CIVRFSGTYKYIF
    CLTRIRANQAGTALIF
    CLVGDHTGGFKTIF
    CSNQAGTALIF
    CVAYSGGYQKVT
    CVGGPYSGAGSYQLTF
    CVLVDSNYQLIW
    CVPMDSNYQLIW
    CVSVDSNYQLIW
    CVVKDSGYALNF
    CVVRDGAGNMLTF
    CVVRDGNDRWGKLQF
    CVVSAEQAGTALIF
    CVVSGSDGQKLLF
    CVVSSSGTYKYIF
    

    Software Downloads




    GETTING HELP

    If you need help regarding technical issues (e.g. errors or missing results) contact Technical Support. Please include the name of the service and version (e.g. NetPhos-4.0) and the options you have selected. If the error occurs after the job has started running, please include the JOB ID (the long code that you see while the job is running).

    If you have scientific questions (e.g. how the method works or how to interpret results), contact Correspondence.

    Correspondence: Technical Support: