منابع مشابه
Haplotype inference by maximum parsimony
MOTIVATION Haplotypes have been attracting increasing attention because of their importance in analysis of many fine-scale molecular-genetics data. Since direct sequencing of haplotype via experimental methods is both time-consuming and expensive, haplotype inference methods that infer haplotypes based on genotype samples become attractive alternatives. RESULTS (1) We design and implement an ...
متن کاملAn Approximation Algorithm for Haplotype Inference by Maximum Parsimony (Class note)
This paper studies haplotype inference by maximum parsimony using population data. We define the optimal haplotype inference (OHI) problem as given a set of genotypes and a set of related haplotypes, find a minimum subset of haplotypes that can resolve all the genotypes. We prove that OHI is NP-hard and can be formulated as an integer quadratic programming (IQP) problem. To solve the IQP proble...
متن کاملComplete Parsimony Haplotype Inference Problem and Algorithms
Haplotype inference by pure parsimony (HIPP) is a wellknown paradigm for haplotype inference. In order to assess the biological significance of this paradigm, we generalize the problem of HIPP to the problem of finding all optimal solutions, which we call complete HIPP. We study intrinsic haplotype features, such as backbone haplotypes and fat genotypes as well as equal columns and decomposabil...
متن کاملHaplotype Inference by Pure Parsimony via Genetic Algorithm
Haplotypes are specially important in the study of complex diseases since they contain more information about gene alleles than genotype data. However, getting haplotype data via experiments methods is techniquely difficult and expensive. Thus, haplotype inference through computational methods is practical and attractive. There are several models for inferrings haplotype from population genotyp...
متن کاملToward an algebraic understanding of haplotype inference by pure parsimony.
Haplotype inference by pure parsimony (HIPP) is known to be NP-Hard. Despite this, many algorithms successfully solve HIPP instances on simulated and real data. In this paper, we explore the connection between algebraic rank and the HIPP problem, to help identify easy and hard instances of the problem. The rank of the input matrix is known to be a lower bound on the size an optimal HIPP solutio...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Bioinformatics
سال: 2003
ISSN: 1367-4803,1460-2059
DOI: 10.1093/bioinformatics/btg239