htSNPer statistics

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htSNPer specifications


Unique identifier OMICS_25310
Name htSNPer
Software type Application/Script
Interface Graphical user interface
Restrictions to use Academic or non-commercial use
Input data A simple flat-file.
Input format TXT
Operating system Unix/Linux
Programming languages Java
Computer skills Medium
Maintained No


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Publication for htSNPer

htSNPer in publications

PMCID: 2838785
PMID: 20300519
DOI: 10.1371/journal.pone.0009684

[…] novel snp not reported in public database before., based on the above sequencing data, linkage disequilibrium analysis results showed that all detected snps located in the same haploblock (). the htsnper1.0 software was used to pick out the tagsnps, and finally four snps were selected as tagsnps, including rs2236660, rs2236658, rs10892958 and rs1461496 (). because the sequences around […]

PMCID: 2749056
PMID: 19712447
DOI: 10.1186/1471-2105-10-269

[…] each iteration was recorded to assess robustness of block partitioning algorithms., to obtain the tagging snps that are required to describe all haplotype variations within a block, we employed the htsnper software []. the htsnper software incorporates an efficient branch and bound algorithm to find the exact solution of the minimum htsnp selection problem. we used default settings of htsnper, […]

PMCID: 2547855
PMID: 18759977
DOI: 10.1186/1471-2164-9-405

[…] those given by limited haplotype diversity methods. additionally, future work could consider the comparison between blocking and using tagging snps. two useful approaches, haploblockfinder [] and htsnper [], produce both haplotype or ld blocks, and tagging snps. as they yield block partitions similar to those of methods already covered by haploview and hapblock, they were not considered here, […]

PMCID: 1829402
PMID: 17381242
DOI: 10.1371/journal.pgen.0030046

[…] example, our method can be used in wga studies by the following procedures: (1) haplotype reconstruction (softwares are available, such as haplotyper [] or phase []) and haplotype block partition (htsnper [] or haploblockfinder []) for whole genome genotype data; (2) in each haplotype block, reconstruct the hierarchical tree within each of the sliding windows using the weighted haplotype […]

PMCID: 1698582
PMID: 17137522
DOI: 10.1186/1471-2105-7-525

[…] distribution of snps for any genomic region of interest. haploview [] is a standalone application that performs ld and haplotype block analysis on publicly available or user supplied genotype data. htsnper1.0 [] and haploblock [] can also be used to analyze genotype data supplied by users. haploblockfinder [] is a web-based tool that allows for the inference of haplotype blocks and tag snp […]

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htSNPer institution(s)
National Laboratory of Medical Molecular Biology; Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College (PUMC), Beijing, China; MOE Key Laboratory of Bioinformatics/Department of Automation, Tsinghua University, Beijing, China; Chinese National Human Genome Center, Beijing, China
htSNPer funding source(s)
Supported in part by China National Key Program on Basic Research (Grant G1998051003 and 2004CB518605), China National HighTech R&D Program (Grant 863-102-10-03-05), and NSFC (Grants 39625007 and 39993420, 60275007 and 60234020).

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