منابع مشابه
Generic ILP vs Specialized 0-1 ILP for Haplotype Inference
Haplotype inference is an important and computationally challenging problem in genetics. A well-known approach to haplotype inference is pure parsimony (HIPP). Despite being based on a simple optimization criterion, HIPP is a computationally hard problem. Recent work has shown that approaches based on Boolean satisfiability namely pseudo-Boolean optimization (PBO), are very effective at tacklin...
متن کاملSelecting Reads for Haplotype Assembly
Haplotype assembly or read-based phasing is the problem of reconstructing both haplotypes of a diploid genome from next-generation sequencing data. This problem is formalized as the Minimum Error Correction (MEC) problem and can be solved using algorithms such as WhatsHap. The runtime of WhatsHap is exponential in the maximum coverage, which is hence controlled in a pre-processing step that sel...
متن کاملHigh-Performance Haplotype Assembly
The problem of Haplotype Assembly is an essential step in human genome analysis. It is typically formalised as the Minimum Error Correction (MEC) problem which is NP-hard. MEC has been approached using heuristics, integer linear programming, and fixedparameter tractability (FPT), including approaches whose runtime is exponential in the length of the DNA fragments obtained by the sequencing proc...
متن کاملTumor Haplotype Assembly Algorithms for Cancer Genomics
The growing availability of inexpensive high-throughput sequence data is enabling researchers to sequence tumor populations within a single individual at high coverage. But, cancer genome sequence evolution and mutational phenomena like driver mutations and gene fusions are difficult to investigate without first reconstructing tumor haplotype sequences. Haplotype assembly of single individual t...
متن کاملComparing ASP, CP, ILP on Haplotype Inference by Pure Parsimony
We study three declarative programming paradigms, Answer Set Programming (ASP), Constraint Programming (CP), and Integer Linear Programming (ILP), on a challenging application: Haplotype Inference by Pure Parsimony (HIPP). We represent HIPP in each formalism in a systematic way, compare the formulations both from the point of view of knowledge representation (e.g., how easy it is to represent s...
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: BMC Bioinformatics
سال: 2018
ISSN: 1471-2105
DOI: 10.1186/s12859-018-2012-x