Usage overview

  • All the programs available here expect plain text files as input (option save as text on your text processor or tabulator).
  • You should upload the data files to the appropriate program, run the program and then you obtain a page with a link (click it) to the results file(s). When you see the results file save it using the save as command of you browser.
  • Typically the results files are deleted after 48 hours, therefore if you have not saved your results file you will need to rerun the programs.

1. The data files should be in UNIFORMAT (version 3):

identifier {white space or tab mark} allele,allele [|allele,allele ...][{white space or tab mark} allele, allele...][{white space or tab mark}#comments]

with commas ‘,‘ separating alleles, vertical bars ‘|‘ separating alternative allele pairs and white space {or tab mark} separating loci. See below for examples.

2. The filename should not contain spaces and it is better to avoid accented characters, use underscore or dash to separate parts of the filename. The suggested form for the filename is:
four parts separated by underscores ending with .unif, as in

3. Please run the Uniformate to validate the data file and check the conformity of your data to UNIFORMAT before running other programs.

4. The kit description, reactivity data and substitution files are described in the pages of the corresponding utilities

UNIFORMAT syntax examples

id	A*01,A*02:01	k-,k+	# a simple double heterozyguous

id	@	k+,k-	# an untyped case for first locus

# a homozyguous-or-blank-heterozyguous for the second locus
id	A*02,A*11	k+

# a real homozygous for first locus and a multiple allele in second locus
id	A*01,A*01	B*07:02,B*14:01&B*14:02&B*14:05&B*14:09

# a case of multiple allele pairs for a locus
id	B*07:02,B*14:01|B*07:02,B*14:02|B*07:02,B*14:05|B*07:02,B*14:09

# a case where the haplotype phase is known (e.g. family data)
# a phased haplotype is treated like an allele by UNIFORMAT  
id	A*01~B*08~DRB1*01,A*03~B*07~DRB1*15

Example of a file for one locus HLA data

sid_0001	A*68,A*03
sid_0008	A*02,A*24
sid_0015	A*03,A*33
sid_0022	A*24,A*68
sid_0029	blank,A*02|A*02,A*02
sid_0036	A*24,A*30
sid_0043	A*03,A*31
sid_0050	A*02,A*26
sid_0057	blank,A*02|A*02,A*02
sid_0064	A*02,A*23
sid_0071	blank,A*02|A*02,A*02
sid_0078	A*03,A*01
sid_0085	blank,A*24|A*24,A*24
sid_0092	A*24,A*01
sid_0099	A*02,A*24
sid_0106	blank,A*02|A*02,A*02
sid_0113	A*02,A*24
sid_0120	A*02,A*25
sid_0127	A*68,A*26
sid_0134	A*03,A*01
sid_0141	A*02,A*33
sid_0148	A*24,A*31
sid_0155	A*03,A*31
sid_0162	A*02,A*68
sid_0169	A*02,A*11

Download the data file

Example of a file for 3 loci HLA data

hhrv_id195	blank,A*02:01|A*02:01,A*02:01	blank,B*44:03|B*44:03,B*44:03	blank,DRB1*07:01|DRB1*07:01,DRB1*07:01
hhrv_id454	A*02:01,A*23:01|A*02:01,A*23:17	B*27:05,B*44:03|B*27:13,B*44:03	DRB1*07:01,DRB1*11:04
hhrv_id642	A*66:01,A*31:08|A*31:08,A*66:08	B*27:05,B*07:02|B*27:05,B*07:61|B*27:13,B*07:02|B*27:13,B*07:61	DRB1*01:01,DRB1*16:02
hhrv_id830	A*02:01,A*26:01	B*07:02,B*38:01|B*07:61,B*38:01	DRB1*13:01,DRB1*15:01
hhrv_id1018	A*02:01,A*03:01	B*40:01,B*44:02|B*40:01,B*44:19N	DRB1*07:01,DRB1*15:01
hhrv_id1206	A*03:01,A*11:01	B*07:02,B*35:03|B*07:61,B*35:03	DRB1*15:01,DRB1*11:01
hhrv_id1394	blank,A*68:01|blank,A*68:11N|A*68:01,A*68:01|A*68:01,A*68:11N|A*68:11N,A*68:11N	B*15:01,B*44:02|B*15:01,B*44:19N	DRB1*04:01,DRB1*11:01
hhrv_id1582	A*24:02,A*03:01	B*07:02,B*18:01|B*07:02,B*18:17N|B*07:61,B*18:01|B*07:61,B*18:17N	DRB1*07:01,DRB1*11:04
hhrv_id1771	A*24:02,A*25:01	B*07:02,B*18:01|B*07:02,B*18:17N|B*07:61,B*18:01|B*07:61,B*18:17N	DRB1*13:01,DRB1*15:01
hhrv_id1959	A*24:02,A*01:01	B*15:01,B*13:02	DRB1*07:01,DRB1*11:01
hhrv_id2066	A*02:01,A*32:01	B*15:01,B*44:02|B*15:01,B*44:19N	DRB1*13:03,DRB1*11:04
hhrv_id2334	A*03:01,A*25:01	B*07:02,B*18:01|B*07:02,B*18:17N|B*07:61,B*18:01|B*07:61,B*18:17N	DRB1*01:01,DRB1*13:01
hhrv_id2522	A*24:02,A*03:01	blank,B*13:02|B*13:02,B*13:02	DRB1*07:01,DRB1*14:01|DRB1*07:01,DRB1*14:54
hhrv_id2710	A*01:01,A*68:01	B*13:02,B*51:01	DRB1*07:01,DRB1*12:01|DRB1*07:01,DRB1*12:06|DRB1*07:01,DRB1*12:10|DRB1*07:01,DRB1*12:17
hhrv_id2899	A*03:01,A*01:01	B*57:01,B*35:01|B*57:01,B*35:42	DRB1*07:01,DRB1*13:02
hhrv_id3087	A*24:02,A*03:01	B*15:01,B*07:02|B*15:01,B*07:61	DRB1*15:01,DRB1*04:01
hhrv_id3275	A*02:01,A*24:02	B*13:02,B*18:01|B*13:02,B*18:17N	DRB1*07:01,DRB1*11:04
hhrv_id3463	A*02:01,A*03:01	B*51:01,B*07:02|B*51:01,B*07:61	DRB1*15:01,DRB1*09:01
hhrv_id3651	A*02:01,A*03:01	B*35:01,B*50:01|B*35:42,B*50:01	DRB1*01:01,DRB1*03:01
hhrv_id3839	A*24:02,A*03:01	B*35:01,B*08:01|B*35:42,B*08:01	DRB1*01:01,DRB1*03:01

Download the data file

Example of a file for 2 loci; one HLA locus and one disease marker

ds871_id_0001	DQB1*03,DQB1*05	+,+
ds871_id_0012	DQB1*05,DQB1*02	+,-
ds871_id_0023	DQB1*06,DQB1*03	-,-
ds871_id_0034	DQB1*06,DQB1*05	+,+
ds871_id_0045	DQB1*06,DQB1*02	+,+|+,blank
ds871_id_0056	DQB1*05,DQB1*02	+,-
ds871_id_0067	DQB1*06,DQB1*03	+,-
ds871_id_0078	DQB1*06,DQB1*04	+,+
ds871_id_0089	blank,DQB1*06|DQB1*06,DQB1*06	+,-
ds871_id_0100	DQB1*03,DQB1*02	-,-
ds871_id_0111	DQB1*03,DQB1*05	+,+
ds871_id_0122	blank,DQB1*03|DQB1*03,DQB1*03	+,-
ds871_id_0133	DQB1*06,DQB1*05	+,-
ds871_id_0144	DQB1*03,DQB1*05	+,-
ds871_id_0155	blank,DQB1*03|DQB1*03,DQB1*03	+,-
ds871_id_0166	blank,DQB1*06|DQB1*06,DQB1*06	+,-
ds871_id_0177	DQB1*03,DQB1*02	+,+|+,blank
ds871_id_0188	DQB1*06,DQB1*03	+,-
ds871_id_0199	DQB1*05,DQB1*02	+,+|+,blank
ds871_id_0210	DQB1*06,DQB1*05	+,-

Download the data file


A tutorial for UNIFORMAT formatting and for using the Gene[rate] programs presented during the 16th IHIWC, Liverpool, May 2012. The new Basic statistics tool simplifies and avoids some operations presented in the tutorial: give it a try.

Preferred citations

Nunes JM, Buhler S, Roessli D, Sanchez-Mazas A and the HLA-net 2013 collaboration (2014) The HLA-net GENE[RATE] pipeline for effective HLA data analysis and its application to 145 population samples from Europe and neighbouring areas. Tissue Antigens 83: 307-323.

The formal description of UNIFORMAT current version 3 is Nunes JM (2015) Using UNIFORMAT and GENE[RATE] to Analyze Data with Ambiguities in Population Genetics. Evolutionary Bioinformatics Suppl. 2 19-26.

The formal description of UNIFORMAT first version is Nunes JM. Tools for analysing ambiguous HLA data. Tissue Antigens. 2007 Apr;69 Suppl 1:203-5. PubMed PMID: 17445201.

3 comments on “Overview

  1. Bushra_Al Hadra

    What is the right syntax of a homozygous locus? Is it for instance: B*51:01,B*51:01
    or B*51:01,blank.

    Thanks in advance!

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