Tools for handling and analysing data with ambiguities

Usage summary
Preferred citation

Usage summary

The programs accessible on the left menu 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.

— The data files should be in UNIFORMAT (version 2):

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

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

— To check the conformity of your data to UNIFORMAT, please run the Uniformate tool to validate the data file before running other programs.

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


	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*14:14&B*14:46&B*14:54

	# a case of multiple allele pairs for a locus
	id	B*07:02,B*14:01|B*07:02,B*14:14|B*07:02,B*14:46|B*07:02,B*14:54

— An example of a file for one locus HLA data
— An example of a file for 3 loci HLA data
— An example of a file for 2 loci; one HLA locus and one disease maker


— A tutorial for UNIFORMAT formatting and the Gene[rate] programs presented during the 16th IHIWC, Liverpool, May 2012

Preferred citation

— JM Nunes. 2006. Generate: tools for analysis and handling of data with ambiguities. Laboratory of Anthropology, Genetics and Peopling History, University of Geneva, Switzerland.

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.