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A Comparison of Several Algorithms for the Single Individual SNP Haplotyping Reconstruction Problem

Motivation: Single Nucleotide Polimorfisms are the most common form of variation in human DNA. They are involved in many research fields from molecular biology to medical therapy. The technological opportunity to deal with long DNA sequences using shotgun  sequencing raised the problem of fragment recombination. In this direction the Single Individual Haplotyping (SIH) problem has received more attention in last few years.

Results: In this paper we survey seven of the most recent approaches to the SIH problem and make an extensive evaluation of them using real human haplotype data from the HapMap project. We also implemented a data generator tailored on current shotgun sequencing technology that use haplotypes from the HapMap project.

Availability: The data we used to compare the algorithms are available on demand since we think they represent an important benckmark that can be used to easily compare novel algorithmic ideas with the state of the art. Moreover, we had to reimplement six of the surveyed algorithms because the original code was not available to us. Five of these algorithms and the data generator used in this paper, endowed with a Web interface are available at  http://bioalgo.iit.cnr.it/rehap


2010

Autori IIT:

Tipo: TR Rapporti tecnici
Area di disciplina: Computer Science & Engineering
IIT TR-05/2010

Attività: Biologia computazionale