Shorelines of islands of tractability: algorithms for parsimony and minimum perfect phylogeny haplotyping problems.
IEEE/ACM Trans Comput Biol Bioinform
; 5(2): 301-12, 2008.
Article
em En
| MEDLINE
| ID: mdl-18451439
ABSTRACT
The problem Parsimony Haplotyping (PH) asks for the smallest set of haplotypes which can explain a given set of genotypes, and the problem Minimum Perfect Phylogeny Haplotyping (MPPH) asks for the smallest such set which also allows the haplotypes to be embedded in a perfect phylogeny, an evolutionary tree with biologically-motivated restrictions. For PH, we extend recent work by further mapping the interface between ;;easy'' and ;;hard'' instances, within the framework of (k,l)-bounded instances where the number of 2's per column and row of the input matrix is restricted. By exploring, in the same way, the tractability frontier of MPPH we provide the first concrete, positive results for this problem. In addition, we construct for both PH and MPPH polynomial time approximation algorithms, based on properties of the columns of the input matrix.
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Filogenia
/
Algoritmos
/
Haplótipos
Tipo de estudo:
Risk_factors_studies
Idioma:
En
Ano de publicação:
2008
Tipo de documento:
Article