IMGT/PRIMER-DB Documentation
IMGT/PRIMER-DB Documentation
 
http://www.imgt.org


Introduction
IMGT/PRIMER-DB definitions
IMGT/PRIMER-DB accession numbers
IMGT/PRIMER-DB query
Query
Results
IMGT/PRIMER-DB cards
IMGT/PRIMER-DB Primer Localization
IMGT/PRIMER-DB Comparison Sequence

Introduction

IMGT/PRIMER-DB definitions

IMGT/PRIMER-DB accession numbers

Each IMGT/PRIMER-DB primer, set or couple, is identified by a unique IMGT/PRIMER-DB accession number.

IMGT/PRIMER-DB Primer accession number Unique identifier of each primer in IMGT/PRIMER-DB.
Consists of 3 letters "IPP" (for IMGT/PRIMER-DB Primer) and 6 numbers.
IMGT/PRIMER-DB Set accession number Unique identifier of each set in IMGT/PRIMER-DB.
Consists of 3 letters "IPS" (for IMGT/PRIMER-DB Set) and 6 numbers.
IMGT/PRIMER-DB Couple accession number Unique identifier of each couple in IMGT/PRIMER-DB.
Consists of 3 letters "IPC" (for IMGT/PRIMER-DB Couple) and 6 numbers.

IMGT/PRIMER-DB query


Each IMGT/PRIMER-DB primer, set or couple, identified by an IMGT/PRIMER-DB accession number is described in an IMGT/PRIMER-DB Primer cards, IMGT/PRIMER-DB Set cards and IMGT/PRIMER-DB Couple cards, respectively.

Query

Two types of query are available:

Results

The resulting page displays:

IMGT/PRIMER-DB cards

  • IMGT/PRIMER-DB Primer card
    1. PRIMER CATALOGUE
      - IMGT/PRIMER-DB Primer accession number: Unique identifier of each primer in IMGT/PRIMER-DB
      - IMGT/PRIMER-DB entry date
      - IMGT/PRIMER-DB update
      - IMGT/PRIMER-DB Primer definition: Automatically composed of the species name followed by the IMGT gene and allele name and the primer orientation.
      - Bibliographic references: 3 possibilities:
      • PMID: refers to the PubMed ID number (hyperlink to the article).
      • Book: primer described in a book.
      • EUROGENTEC: primer described by EUROGENTEC.
      - Catalogue comments

    2. PRIMER CHARACTERISTICS
      - IMGT/PRIMER-DB Primer sequence: Given in bold CAPITAL letters.
        Underline indicates restriction sites (described in "PRIMER DESCRIPTION").
        Blinking
        nucleotides
        indicate nucleotide differences between the primer sequence and the IMGT/LIGM-DB reference sequence (described in "PRIMER DESCRIPTION").
        Italics indicates additional nucleotides, not present in the IMGT/LIGM-DB reference sequence, such as sequence linkers, restriction sites, etc.
      - IMGT/PRIMER-DB Sequence length: In number of nucleotides.
      - IMGT/PRIMER-DB Primer orientation: "Sense" or "Antisense" (by comparison with the gene transcription orientation).
      - IMGT/LIGM-DB reference sequence Accession number:
        Unique IMGT/LIGM-DB accession number of the IMGT reference sequence which allowed the definition (in PRIMER CATALOGUE), classification (in PRIMER CLASSIFICATION) and the label description (in PRIMER DESCRIPTION) of the primer.
      Click on the IMGT/LIGM-DB reference sequence Accession number to access the IMGT/LIGM-DB flat file.
      - IMGT/LIGM-DB reference sequence Primer position: Primer position (start-end) in the IMGT/LIGM-DB flat file reference sequence.
      - Characteristics comments

    3. PRIMER CLASSIFICATION
      - IMGT/LIGM-DB reference sequence Species: Latin name of species related to the primer, sometimes followed by common name between brackets.
      - IMGT/LIGM-DB reference sequence Classification: CLASSIFICATION comprises IMGT group, IMGT subgroup or cluster, IMGT gene name and IMGT allele name.
        Click on the IMGT gene name to view IMGT Colliers de Perles.
      Click on the IMGT allele name to view IMGT Alignments of alleles.
      - Classification comments and specificity: Specificity as described experimentally or deduced from sequence comparison, with a reference for the source of information.

    4. PRIMER DESCRIPTION
      - IMGT/PRIMER-DB Primer labels: IMGT standardized labels used to describe the primer.
        For V-DOMAIN AND C-DOMAIN primers, amino acids are described with the IMGT unique numbering for V-DOMAIN and IMGT unique numbering for C-DOMAIN, respectively. Example: "AA_IMGT 1..8".
      - Differences between the IMGT/LIGM-DB reference sequence and the primer sequence.
      - Restriction enzyme name: Restriction site sequence and enzyme name: Example: "GAATTC EcoRI".
      - Restriction site position: Restriction site position in the primer.
      - Purification methods
      - Keywords
      - Description comments

    1. IMGT/PRIMER-DB set
      Provides the list of the accession numbers of the IMGT/PRIMER-DB sets to which a primer belongs.
    Click on the IMGT/PRIMER-DB Set accession number to access the corresponding IMGT/PRIMER-DB Set card.

  • IMGT/PRIMER-DB Set card
    1. SET CATALOGUE
      - IMGT/PRIMER-DB Set accession number: Unique identifier of each set in IMGT/PRIMER-DB

    2. SET CHARACTERISTICS
      - IMGT/PRIMER-DB Set orientation: "Sense" or "Antisense". Defined by the primer orientation, common to all primers in the set.

    3. SET CLASSIFICATION
      - Species: Species Latin name: Defined by the primer species, common to all primers in the set.
      - IMGT group: Defined by the primer IMGT group, common to all primers in the set.

    4. SET DESCRIPTION
      Provides the list of the IMGT/PRIMER-DB Primer accession numbers of all primers contained in the selected IMGT/PRIMER-DB set, with IMGT subgroup, IMGT gene name and IMGT allele name information.
      Click on an IMGT/PRIMER-DB Primer accession number to access the corresponding IMGT/PRIMER-DB Primer card.

    5. IMGT/PRIMER-DB couples
      Provides the list of the accession numbers of the IMGT/PRIMER-DB couples to which a set belongs.
      Click on the IMGT/PRIMER-DB Couple accession number to access the corresponding IMGT/PRIMER-DB Couple card.

    6. IMGT/PRIMER-DB Couple card
      • The IMGT/PRIMER-DB Couple card provides:
        - the IMGT/PRIMER-DB accession numbers of the Sense IMGT/PRIMER-DB sets and Antisense IMGT/PRIMER-DB sets,
        - the bibliographical references,
        - the list of the IMGT/LIGM-DB accession numbers of the resulting sequences from this couple, with between parentheses, the number of sequences.
        Click on an IMGT/LIGM-DB Accession number to access the flat file in IMGT/LIGM-DB.


    IMGT/PRIMER-DB Primer Localization


    IMGT/PRIMER-DB Primer Sequence Comparison


    Created      : 15/07/2002
    Last update : 10/04/2007