Introduction

The IMGT/PRIMER-DB database provides standardized information on oligonucleotides or primers of the immunoglobulins (IG) and T cell receptors (TR).
The IMGT/PRIMER-DB database is part of IMGT, the international ImMunoGeneTics information system^® http://imgt.cines.fr
The information provided by IMGT/PRIMER-DB is particulary useful for the studies on the expression of IG and TR in normal and pathological situations and for the combinatorial library, scFv, phage display and microarray biotechnologies.

IMGT/PRIMER-DB definitions

IMGT/PRIMER-DB contains information on primers and combinations of primers described as "sets" and "couples".

• An IMGT/PRIMER-DB primer is an oligonucleotide defined, classified and described by comparison to an IMGT/LIGM-DB reference sequence.

  The definition, taxonomy species, classification (IMGT group, IMGT subgroup, IMGT gene, IMGT allele) and label description of an IMGT/PRIMER-DB primer are those of the IMGT/LIGM-DB reference sequence, and not those of the PCR amplification products.

  This provides the following advantages for the data standardization:
  

  • IMGT/PRIMER-DB primers can easily be compared to data from the other IMGT databases (IMGT/LIGM-DB, IMGT/GENE-DB, IMGT/3Dstructure-DB), IMGT Web resources (IMGT Repertoire) and tools (IMGT/V-QUEST, IMGT/PhyloGene). These data are described according to the standardized rules of the IMGT Scientific chart, based on IMGT-ONTOLOGY.
    
  • IMGT/PRIMER-DB primer definition, classification and description are independent from the experimental conditions, from DNA sources and from the different combinations (sets and couples) in which the primer can be used. That means that (i) the specificity of a primer (subgroup, gene or allele specific) which is either described experimentally or deduced from sequence comparison is not used for the primer classification, although these data are provided in the IMGT/PRIMER-DB Primer card in Classification comments and specificity, (ii) the sequences resulting from the PCR amplifications are uniquely associated to the couples.

• An IMGT/PRIMER-DB set consists of IMGT/PRIMER-DB primers sharing identical properties (species, group and orientation). An IMGT/PRIMER-DB set may be composed of only one IMGT/PRIMER-DB primer.

• An IMGT/PRIMER-DB couple consists of sets of opposite orientation for which IMGT/LIGM-DB sequences are known (or expected). An IMGT/PRIMER-DB couple comprises a Sense IMGT/PRIMER-DB set and an Antisense IMGT/PRIMER-DB set. For example, an IMGT/PRIMER-DB couple may consists of Sense IMGT/PRIMER-DB sets of V regions associated to Antisense IMGT/PRIMER-DB sets of C regions.
  

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:

Search can be made directly by the IMGT/PRIMER-DB Primer accession number, IMGT/PRIMER-DB Set accession number or IMGT/PRIMER-DB Couple accession number.

This query gives access to the corresponding IMGT/PRIMER-DB Primer card, IMGT/PRIMER-DB Set card or IMGT/PRIMER-DB Couple card.

Primers may be selected on the following criteria: Species, IMGT group and Primer orientation

First, select the Species, IMGT group and Primer orientation. The page will reload automatically with your choice.

You can: either "Display group list". This will display the list of primers corresponding to your species and group selection or display from the group list, only the primers which correspond to an additional selection on "IMGT subgroup", "IMGT gene name" or "IMGT allele name": (1) choose the selection, (2) select the appropriate IMGT subgroup, IMGT gene name IMGT allele name, and (3) click on "Display selection".

Results

The resulting page displays:

- your selection at the top of the page, so you can check your own queries.
- the number of IMGT/PRIMER-DB primers which match your selection.
- the list of the primers which match your selection, with their main characteristics.

A button allows to classify that list by IMGT/PRIMER-DB Primer accession numbers, IMGT subgroups, IMGT gene names or IMGT allele names.

IMGT/PRIMER-DB Primer accession number:	Click on t>e IMGT/PRIMER-DB Primer accession number to get access to the IMGT/PRIMER-DB Primer card
Species:	Latin name is according to the IMGT Taxonomy (IMGT Repertoire).
IMGT/PRIMER-DB Primer orientation:	"Sense" or "Antisense" is by comparison with the gene transcription orientation.
IMGT group
IMGT subgroup:	Only for variable genes
IMGT gene name:	Gene name is according to the IMGT nomenclature: Nomenclature (IMGT Index), IMGT gene nomenclature (IMGT Scientific chart), and as used in IMGT Repertoire (Germline gene tables) and IMGT/GENE-DB.
IMGT allele name:	Allele name is according to the IMGT nomenclature: Allele (IMGT Index), IMGT allele nomenclature (IMGT Scientific chart), and as used in IMGT Repertoire (Alignments of alleles) and IMGT/GENE-DB.

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

   
   

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.

   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

Each IMGT/PRIMER-DB primer, identified by an accession number, can be localized into the corresponding IMGT Sequence.

The localization of the oligonucleotides will be done on the gene sequences characterized in IMGT/GENE-DB (IMGT/GENE-DB is the IMGT genome database of immunoglobulins and receptors T).

The localization take into account information (annotations, "labels", positions according to single classification IMGT) which will be extracted from IMGT/LIGM-DB (IMGT/LIGM-DB is the IMGT sequence database of the immunoglobulines and the receptors T).

Click on the IMGT/PRIMER-DB "Primer Localization" button to get access to the IMGT/PRIMER-DB Primer Localization page.

The IMGT/PRIMER-DB Localization provides :
- the Primer Information : Accession number, Species, IMGT Group, IMGT Gene, IMGT Allele and Primer Orientation,
- the unique IMGT/LIGM-DB accession number of the IMGT reference sequence,


Click on the IMGT/LIGM-DB Accession number to access the flat file in IMGT/LIGM-DB.



- the IMGT/PRIMER-DB Primer Localization,

IMGT/PRIMER-DB Primer Sequence Comparison

You can search an IMGT/PRIMER-DB primer sequence directly by keyboarding your primer sequence.

The comparison sequence with all the IMGT/Primer-DB sequences is made using fasta35*, a program which compares a protein sequence to a protein sequence database or a DNA sequence to a DNA sequence database using the FASTA algorithm (Pearson and Lipman, 1988, Pearson, 1996). Search speed and selectivity are controlled with the ktup(wordsize) parameter. For protein comparisons, ktup = 2 by default; ktup =1 is more sensitive but slower. For DNA comparisons, ktup=6 by default; ktup=3 or ktup=4 provides higher sensi- tivity; ktup=1 should be used for oligonucleotides (DNA query lengths < 20).





The IMGT/PRIMER-DB Fasta Result Page provides:

- The IMGT/PRIMER-DB Primer accession number
- The Species
- The Smith-Waterman Score
- The Percentage identity
- The Overlap - The alignment



Fasta35 is used with the following command line options:

-ktup: Search speed and selectivity are controlled with the ktup(wordsize) parameter. ktup=1 should be used for oligonucleotides (DNA query lengths < 20).

-c: Set to 1 to optimize every sequence in a database.

-A: Force Smith-Waterman alignments for fasta3 DNA sequences. By default, only fasta3 protein sequence comparisons use Smith-Waterman alignments.

-b: Number of sequence scores to be shown on output. Set to 10.

-E: Limit the number of scores and alignments shown based on the expected number of scores. Used to override the expectation value of 10.0 used by default.Set to 10. -m: Specify alignment type: 0, 1, 2, 3, 4, 5, 6, 9, 10. Set to 0.

-z: Set to 0. z 0 estimates the significance of the match from the mean and standard deviation of the library scores, without correcting for library sequence length.

* Copyright 1988, 1991, 1992, 1994, 1995, 1996, 1999 by William R. Pearson and the University of Virginia. All rights reserved.

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