Ali Reza Khanteymoori

Haplotype Reconstruction

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Haplotype Reconstruction

Do you know that more than 99% of human genome are completely identical? So, all differences between us come from that little variations. Undoubtedly, these variations have an important role in complex diseases. During some international projects (such as HapMap project), researchers have concentrated on analyzing of genome sequences.

Single nucleotide polymorphisms (SNPs) is a variation in a single nucleotide that occurs at a specific position in the genome. Haplotype is a sequence of SNPs measures (alleles) in a chromosome which involves more valuable information than SNPs.

In diploid organisms such as humans, chromosomes are in pairs which one comes from father and the other comes from mother. On the other hand, the combination of two haplotypes of a pair of chromosome is called genotype. Haplotypes have more information than genotypes but require more complicated investigates to determination. Therefore, many computational methods have been proposed to solve this problem. Haplotype inference and Single individual haplotypes (SIHs) are two main approaches which the first generates haplotypes from genotype samples and the latter reconstructs haplotypes from a set of fragments provided by sequencing.

In SIH which we have currently focused, the input data involves two types of errors called missing value and sequencing errors. It has been proved that correcting possible fragments errors in the presence of gaps is NP-Hard problem. Four problem formulation have been suggested to solve SIH which are involved minimum error correction (MEC), minimum fragment removal (MFR), minimum SNP removal (MSR) and longest haplotype reconstruction (LHR).

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