 Human
Leukocyte Antigene (HLA) genes are crucial determinant of transplant
rejection and susceptibility to a variety of autoimmune-related diseases.
However, large-scale and accurate typing of HLA alleles is laborious and
expensive. We developed an algorithm for selecting a small subset of
Single
Nucleotide Polymorphisms (SNPs), called tag SNPs, which is able to
capture HLA alleles. The HLA alleles can be indirectly predicted by alleles
of these tag SNPs without performing direct HLA typing.
(source: wikipedia)
References:
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Huang, Y.-T.
and Tsai, C.-C., “HLATag: Selection of Tag SNPs for
Capturing Human Leukocyte Antigenes”
Manuscript.
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A
power point presentation |
HLATag:
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HLATag
is implemented in C.
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Source code and experimental data:
the
source code of the two-stage
algorithm and the HLA and SNP data sets of all populations are compressed by
WinZip.
A binary executable file (HLATag) compiled on Linux platform is also
included. You might have to use chmod to make it executable.
A readme file contains instructions for running the program.
Simple usage scenario:
HLATag <Input file> <SNP ID>
HLATag YRI_HLAA.txt YRI_RSN_A.txt
and an output file tagSNP.out will be generated.
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Input file format: Each row represents the HLA and SNP alleles of
a haplotype. The first column stands for the HLA allele. The second
column, separated by a tab space, stands for the SNP alleles. Each SNP allele
is denoted as 0,1,2,3, and 4, representing missing allele, A, C, G, and T,
respectively. For example, given HLA and SNP alleles of five haplotypes, the input file appears as following
example:
1801 14112
1801 14113
1702 11342
1702 14142
1703
11313
SNP ID format: a list of SNP IDs in each line,
corresponding to each SNP column in the input file.
rs1000
rs1004
rs1005
rs1006
rs1007
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If you encounter any problem, please contact
Yao-Ting Huang (ythuang at cs.ccu.edu.tw).
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