Github for files currently published in the IPD-KIR FTP Directory hosted at the European Bioinformatics Institute
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fasta
msf
pir
xml
Allelelist.100.txt
Allelelist.110.txt
Allelelist.111.txt
Allelelist.120.txt
Allelelist.121.txt
Allelelist.130.txt
Allelelist.140.txt
Allelelist.200.txt
Allelelist.201.txt
Allelelist.210.txt
Allelelist.220.txt
Allelelist.230.txt
Allelelist.240.txt
Allelelist.250.txt
Allelelist.260.txt
Allelelist.270.txt
Allelelist.271.txt
Allelelist.280.txt
Allelelist.txt
Deleted_alleles.txt
KIR.dat
KIR_gen.fasta
KIR_nuc.fasta
KIR_prot.fasta
LICENCE.md
Manual.md
README.md
md5checksum.txt

README.md


IPD-KIR Database

This directory contains data for the IPD-KIR Sequence Database. The database provides a centralised repository for human KIR sequences. Killer-cell Immunoglobulin-like Receptors (KIR) have been shown to be highly polymorphic at the allelic and haplotypic level. KIRs are members of the immunoglobulin superfamily (IgSF) formerly called Killer-cell Inhibitory Receptors. They are composed of two or three Ig-domains, a transmembrane region and cytoplasmic tail which can in turn be short (activatory) or long (inhibitory). The Leukocyte Receptor Complex (LRC) which encodes KIR genes has been shown to be polymorphic, polygenic and complex like the MHC.The database was publically released in February 2003.

  • Updated: 28 June 2003, Release 1.0.0
  • Updated: 24 January 2005, Release 1.1.0
  • Updated: 11 October 2005, Release 1.1.1
  • Updated: 10 March 2006, Release 1.2.0
  • Updated: 23 March 2006, Release 1.2.1
  • Updated: 10 November 2006, Release 1.3.0
  • Updated: 04 June 2007, Release 1.4.0
  • Updated: 18 January 2008, Release 2.0.0
  • Updated: 17 September 2008, Release 2.0.1
  • Updated: 20 February 2009, Release 2.1.0
  • Updated: 25 May 2010, Release 2.2.0
  • Updated: 16 August 2010, Release 2.3.0
  • Updated: 15 April 2011, Release 2.4.0
  • Updated: 11 October 2013, Release 2.5.0
  • Updated: 19 January 2015, Release 2.6.0
  • Updated: 14 July 2017, Release 2.7.0
  • Updated: 16 January 2018, Release 2.7.1
  • Updated: 30 November 2018, Release 2.8.0

Files are currently provided for the nucleotide and protein sequences in FASTA, PIR and MSF format.

For information on the IPD-KIR Sequence Database please see the website at: http://www.ebi.ac.uk/ipd/kir/

For any other information please contact ipd@ebi.ac.uk.


File Formats

The directory also contains the KIR sequences in a number of formats. Within the following folders, the various format types are explained briefly here:

FASTA folder

All files in this folder are provided in the FASTA sequence format. Please note the FASTA format contains no alignment information.

Files designated “X_prot.fasta”, where X is a locus or gene, contain protein sequences. Please note that alleles that contain non-coding variations may be identical at the protein level.

Files designated “X_nuc.fasta”, where X is a locus or gene, contain the nucleotide coding sequences (CDS). Please note that alleles that contain non-coding variations may be identical at the CDS level.

Files designated “X_gen.fasta”, where X is a locus or gene, contain genomic DNA sequences. Please note for alleles that do not possess genomic sequences, there will be no entry in the file.

MSF Folder

All files in this folder are provided in the MSF sequence format.

Files designated “X_prot.msf”, where X is a locus or gene, contain protein sequences. Please note that alleles that contain non-coding variations may be identical at the protein level.

Files designated “X_nuc.msf”, where X is a locus or gene, contain the nucleotide coding sequences (CDS). Please note that alleles that contain non-coding variations may be identical at the CDS level.

Files designated “X_gen.msf”, where X is a locus or gene, contain genomic DNA sequences. Please note for alleles that do not possess genomic sequences, there will be no entry in the file.

PIR

All files in this folder are provided in the PIR sequence format.

Files designated “X_prot.pir”, where X is a locus or gene, contain protein sequences. Please note that alleles that contain non-coding variations may be identical at the protein level.

Files designated “X_nuc.pir”, where X is a locus or gene, contain the nucleotide coding sequences (CDS). Please note that alleles that contain non-coding variations may be identical at the CDS level.

Files designated “X_gen.pir”, where X is a locus or gene, contain genomic DNA sequences. Please note for alleles that do not possess genomic sequences, there will be no entry in the file.

XML

A beta-version of an XML formatted export of the IPD-KIR sequences, both XML and XSD files are provided.

Other Files

The top-level directory contains the following lists;

  • Allelelist.txt and Allelelist.XXXX.txt - a csv file listed all alleles named at the time of the release, the XXXX in the file denotes a particular release. Allelelist.txt is a copy of the latest version.
  • Deleted_alleles.txt - a csv file detailing all deleted allele names, with reasons for the deletion. This list also includes details of any suffix changes.
  • KIR.dat - An EMBL-ENA style format file containing data from the IPD-KIR Database, see http://www.ebi.ac.uk/ipd/imgt/hla/docs/manual.html for further details.
  • KIR_gen.fasta - a copy of the file in the fasta directory, includes the DNA sequence for all alleles, which have genomic sequences available.
  • KIR_nuc.fasta - a copy of the file in the fasta directory, includes the DNA sequence for the CDS sequence of all alleles.
  • KIR_prot.fasta - a copy of the file in the fasta directory, includes the amino acid sequence for all alleles.
  • LICENSE.md - a file detailing the licensing of data included in the IPD-KIR Database.
  • README.md - This README file
  • Manual.md - This is documentation for the KIR.dat file
  • md5checksum.txt - a file detailing md5 checksums for all files in the top-levle directory

CONTACTS

For information on the IPD-KIR Database please see the website at: http://www.ebi.ac.uk/ipd/kir

Additional information on sequence file formats is available from: http://www.ebi.ac.uk/ipd/kir/download.html

For any other information please contact hla@alleles.org.


COPYRIGHT NOTICE

We have chosen to apply the Creative Commons Attribution-NoDerivs License to all copyrightable parts of our databases, which includes the sequence alignments. This means that you are free to copy, distribute, display and make commercial use of the databases in all legislations, provided you give us credit by citing the following;

Robinson J, Halliwell JA, Hayhurst JH, Flicek P, Parham P, Marsh SGE: The IPD and IPD-IMGT/HLA Database: allele variant databases Nucleic Acids Research (2015), 43:D423-431

Robinson J, Malik A, Parham P, Bodmer JG, Marsh SGE: IMGT/HLA - a sequence database for the human major histocompatibility complex Tissue Antigens (2000), 55:280-287

We are strongly opposed to the mirroring of the data contained on our sites, both hla.alleles.org and the IPD Databases, and would ask that rather than mirror the information, appropriate links are provided where applicable.

If you intend to distribute a modified version of our data, you must ask us for permission first, please contact hla [at] alleles [dot] org for further details of how modified data can be reproduced.

If you intend to use any of the data found on our sites for commercial use, we would ask you to consider funding the databases and the work we do. Without continued funding the database cannot be maintained.


DISCLAIMER

Where discrepancies have arisen between reported sequences and those stored in the database, the original authors have been contacted where possible, and necessary amendments to published sequences have been incorporated. Future sequencing may identify errors and the WHO Nomenclature Committee would welcome any evidence that helps to maintain the accuracy of the database. We therefore make no warranties regarding the correctness of the data, and disclaim liability for damages resulting from its use. We cannot provide unrestricted permission regarding the use of the data, as some data may be covered by patents or other rights. Any medical or genetic information is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

We reserve the right to use information about visitors (IP addresses), date/time visited, page visited, referring website, etc. for site usage statistics and to improve our services.