WELCOME!
to IMGT/LIGM-DB

THE INTERNATIONAL IMMUNOGENETICS INFORMATION SYSTEM®

Database contains
251557 sequences
from 368 species

Introduction

IMGT/LIGM-DB is the first database of IMGT®, the international ImMunoGeneTics information system®, the high-quality integrated database specializing in Immunoglobulins (IG), T cell Receptors (TR) and Major Histocompatibility Complex (MHC) molecules of all vertebrate species, created in 1989 by Marie-Paule Lefranc (LIGM, Université Montpellier II, CNRS and on the web since July 1995. IMGT/LIGM-DB is a comprehensive database of Immunoglobulins (IG) and T cell Receptors (TR) from human and other vertebrates, with translation for fully annotated sequences.

Good to know

Open files

• In order to avoid some format problem, please do not open files from IMGT/LIGM-DB query tools with Notepad (Windows), use preferably WordPad or Notepadd++

Browser

• Use preferably Firefox or Chrome.

Query page

Search by

• Accession number

  Accession number is identical to EMBL accession number. Accession number field is case sensitive, use upper case.
  You can search for:

  • a single accession number (ex: M94115)
  • a range of accession numbers starting with a common prefix using '*' as wildcard (ex: M941*)
  • several accession numbers using ';' as separator (ex: M94115; M94116; M94117)
  • the combination of the two cases cited above (ex: M941*; M94349)
  
  
• Annotation level

  You can search for sequences in IMGT/LIGM-DB based on their annotation level: 'keyword level' or 'fully annotated'.
  Fully annotated sequences include sequences automatically annotated by IMGT/Automat and sequences manually annotated by IMGT annotators

• Sequence length

  A sequence can be retrieved by its length in nucleotides. You can search for:

  • sequences longer than X nucleotides (ex : from 1000 to {empty} nt.)
  • sequences shorter than Y nucleotides (ex : from {empty} to 1000 nt.)
  • sequences which length is between X and Y nucleotides (from 150 to 1000 nt.)
  
  
• Definition (part of)

  A sequence can be retrieved by its exact definition or by an exact part of its definition. The definition field is not case sensitive.

Search by IMGT-ONTOLOGY concepts

IDENTIFICATION

• Taxonomy

  Taxonomy in IMGT/LIGM-DB is based on NCBI Taxonomy.
  You can either search by species (taxon directly linked to a sequence) or by taxon (upper level taxons linked indirectly to a sequence by its species).
  You can search for several species/taxons at the same time.
  The search functionality helps you to find a species/taxons typing its scientific or common name.
  

• Molecule type

  Sequences in IMGT/LIGM-DB are either gDNA or cDNA. The sequence molecule type information is part of keyword annotation.

• Configuration type, Gene type, Molecule entity type, Functionality, Chain type, Structure type, Location type

  These sequence informations are part of keyword annotation. You can search for several values of each categories at the same time.

• Other keywords

  This search field contains all the other type of keywords available in IMGT/LIGM-DB. You can search for several values at the same time.

See the full list of standardized IMGT/LIGM-DB keywords

CLASSIFICATION

• IMGT group
• IMGT subgroup
• IMGT gene

  IMGT gene section shows all the values that can be found under IMGT_gene qualifier used for annotation.
  You can only search for one IMGT gene at the same time.
  

• IMGT allele

  IMGT allele section shows all the values that can be found under IMGT_allele qualifier used for annotation.
  You can only search for one IMGT allele at the same time.
  Some of the IMGT allele values are truncated because they are too long (they ends with "..."). Mouse over theses truncated values to see full value.

DESCRIPTION

• Labels

  Labels are part of sequence's manual or automatic annotations.
  You can search for several labels at the same time.
  The search functionality helps you to find a label typing its name.

See the full list of IMGT/LIGM-DB labels

OBTENTION

• Specificity

See the full list of IMGT/LIGM-DB specificities and their sequence repartition

• Disease related

  Disease related information is part of keyword annotation. You can search for several values at the same time.

See the full list of standardized IMGT/LIGM-DB keywords

Search by bibliographical references

• Author
  • Sequences can be retrieved by the name of the author of their associated references. Author field is not case sensitive.
  • Check "first author only" option to restrict your search on on first author only. This option is available only if an author name is entered in author field.
  
  
• Type

  Select 'any' to not restrict your search on one reference type.

• Journal

  This field is shown only if Type field above is set on 'Journal'.

• PMID

  Sequences can be retrieved by their associated reference's PMID, you can enter several PMIDs using ';' as separator

• Year

  Sequences can be retrieved by their associated reference's year. Sequences in IMGT/LIGM-DB are linked to references from 1971 to now.

• Title (part of)

  Sequences can be retrieved by the exact title or a part of the title of their associated references. The title field is not case sensitive.

Result page

Your selection

This section is a summary of your query, detailed field by field.

Your results

This section show the list of sequences retrieved by your query.

Browse and select results

Results are paginated.
Each page show 50 sequences.
The pager first line indicates the total number of sequences retrieved and then the range of displayed sequences.
The pager second line shows the pages you can navigate through to see the retrieved results.

Result table details

• Checkboxes column

  Select all the sequences in the current page ticking the checkbox in the table header.
  Select sequences individually ticking the checkbox in front of the chosen sequences.

• Acc. number column

  This column shows the sequence accession number. Click on accession number to see the IMGT annotation view.

• Species column

  This column shows the sequence's species. Sequences can be linked to several species.

• Definition column

  This column shows the 200 first characters of the sequence definition.

• Annot. level column

  This column shows the sequence's annotation level. Sequences can be annotated at keyword (K) level or fully annotated. Full annotation can be divided in 2 categories, manual (man. annot.) or automatic (auto. annot.)

• Seq. length column

  This column shows the sequence length in nucleotides.

• Flat files column

  This column gives access to the sequence IMGT and EMBL flat files and to the sequence translation.
  Each file can be downloaded individually from each given view. To download more than one file at a time, see "Download files" section below.

Download files

To download multiple sequence flat files:

1. select the sequences you want to download ticking the checkbox in front of the chosen sequences,
2. choose the file format,
3. choose the file type,
4. click on Download button,
5. open/save the file to download.

The downloaded file is a zip file that contains at least 3 files:

• the query summary,
• the list of selected sequences,
• the flat files according to chosen format and type.

File format

Available flat file formats are: IMGT, EMBL, FASTA, Translation and dump.

File type

Available flat file types are:

• 'Split': each sequence in flat format in its own file,
• 'Concatenated': all sequences in flat format in one file.

Extract subsequences

Subsequences are extracted only for manually/automatically annotated sequences.
To extract subsequences:

1. select the sequences for which you want to extract subsequences:
   • ticking the checkbox in front of the chosen sequences,
   • selecting all the sequence on the current page,
   • selecting all the sequence retrieved by your query if the number of sequences does not exceed 60000;
2. choose the labels for which you want to extract subsequences (Note that the proposed label are coding),
3. click on 'Extract' button.

Labels to extract

Not all the labels can be extracted.
Amongst the extractable labels, some are coding, so subsequence translation can be proceeded while some are not.

See the full list of IMGT/LIGM-DB labels

The extraction view

• For extracted subsequences are shown:
  • the list of extracted subsequences for each selected labels,
  • the list of sequences for which selected labels have not been found.
    This means that the sequences are annotated at keyword level only or that the sequences annotations do not contain the selected label
  • the list of labels not found in selected sequences.
• For translated extracted subsequences are shown:
  • the list of extracted and translated subsequences
  • the list of non coding labels (cannot be translated)
  • the list of label not found in selected sequences

You can download extracted subsequences clicking on "Download FASTA" button.
The download file is a zip file that contains

• the query summary
• the list of selected sequences
• the list of selected labels
• the extracted subsequences in FASTA format
• the translated extracted subsequences in FASTA format

The FASTA header contains 15 fields separated by '|' character composed as follow (field marked with * are mandatory):

• IMGT/LIGM-DB accession number*
• allele or gene name (according to IMGT nomenclature)
• species*
• functionality (can take the value F (functional), P (pseudo), ORF, productive or unproductive)
• extracted label*
• location* (according to EMBL format)
• length in nucleotides (also for translated subsequence)
• codon start
• empty (not relevant)
• empty (not relevant)
• empty (not relevant)
• number of amino acids (AA): this field indicates that the sequence is in amino acids
• number of characters in the sequence: nt (or AA)+IMGT gaps=total
• partial (if it is)
• reverse complementary (if it is)

Sequence display

Annotation view

This view displays the sequence information organized according to IMGT-ONTOLOGY concepts.

Flat file view

IMGT

This view display the sequence in IMGT flat format, that show IMGT annotations.

EMBL

This view display the sequence in EMBL flat format.

FASTA

This view display the sequence in FASTA format. Sequences are written in blocks of 60 residues.

The FASTA header contains 4 columns separated by pipes composed as follow

• accession number
• species
• molecule type
• definition

Translation

This view display the sequence translation with various frame representations

Dump

This view display the sequence in a dump format. Sequences are displayed following EMBL SQ lines format.

Program changes

Version 1.2.11 (2023/11/21)

• Repairing the link to IMGT/BlastSearch.

Version 1.2.10 (2023/09/20)

• Maintenance release.
• Allow a direct link to the sequence view using the secondary access number and/or sequence version.

Version 1.2.9 (2021/05/31)

• Change the header of the FASTA sequences when downloading the extraction of labels so that the mention 'partial in' refer to the orientation of the gene and not to the orientation of the sequence.

Version 1.2.8 (2019/06/04)

• Update links to IMGT/V-QUEST.

Version 1.2.7 (2019/01/16)

• Remove bug when linking to accession numbers with a dot character that is not a sequence version separator.

Version 1.2.6 (2018/09/18)

• Provide links in 'Database cross-references' section and for some qualifier values.
• Bug when searching accession numbers with a dot character that is not a sequence version separator.

Version 1.2.5 (2018/03/06)

• Fix bug when using an 'Author' value in 'Search by bibliographical references'.

Version 1.2.4 (2017/11/27)

• Show sequence version in many places and admit usual notation (eg. IMGT000001.1) in query and using direct link

Version 1.2.3 (2017/10/13)

• Solve a bug regarding 'IMGT group' selection

Version 1.2.2 (2016/12/07)

• New page for the list of possible qualifiers.
• Small internal changes.

Version 1.2 (2016/03/03)

• Tables in 'Extract subsequences' now show 'Allele or gene' and 'Functionality' for most of gene entity labels.
• FASTA format header in 'Extract subsequences' has been changed accordingly to IMGT/GENE-DB FASTA format.

Version 1.1 (2015/03/09)

• Improve gene and allele selections.
• Add links to IMGT/BlastSearch and IMGT/V-QUEST in 'Views'.
• Sort values in many lists using (alphanumeric) natural order.
• Show list of labels in 'Extract subsequences' regarding the sequence result set.
• Remove bug in querying by specificities.
• Remove bug when downloading translation file.

Created:

23/07/1995

Maintainers:

Denys Chaume, Nelly Jouffre and Patrice Duroux

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