Journal ArticleDOI
Classification of de Bruijn-based labeled digraphs
Marta Kasprzak,Marta Kasprzak +1 more
TLDR
The current work can be treated as a support in choosing an appropriate combinatorial model, resulting in polynomial time solution of problems related to searching for the Hamiltonian cycle or path, which are strongly NP-hard in general.About:
This article is published in Discrete Applied Mathematics.The article was published on 2018-01-10. It has received 7 citations till now. The article focuses on the topics: Chordal graph & Indifference graph.read more
Citations
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Journal ArticleDOI
Eulertigs: minimum plain text representation of k-mer sets without repetitions in linear time
Sebastian Schmidt,Jarno Alanko +1 more
TL;DR: This work presents a formalisation of arc-centric bidirected de Bruijn graphs and carefully proves that it accurately models the k-mer spectrum of the input.
Journal ArticleDOI
Different DNA Sequencing Using DNA Graphs: A Study
TL;DR: This study aims to investigate the role of DNA sequencing and its representation in the form of graphs in the analysis of different diseases by means ofDNA sequencing.
Book ChapterDOI
Labeled Graphs in Life Sciences - Two Important Applications
TL;DR: A short review of selected applications of labeled graphs in biology and chemistry is given in this paper, where graph theory problems concerning molecules of chemical compounds and DNA sequencing are presented, as well as some graph theoretic problems concerning DNA sequencing.
Posted ContentDOI
Eulertigs: minimum plain text representation of <i>k</i>-mer sets without repetitions in linear time
TL;DR: In this paper , the authors present an algorithm to compute a minimum representation in optimal (linear) time and use it to evaluate the existing heuristics, and carefully prove that it accurately models the k-mer spectrum of the input.
Journal ArticleDOI
A method for constructing artificial DNA libraries based on generalized de Bruijn sequences
TL;DR: In general, the algorithm can be used to build a chain over any alphabet of even size with defined binary symmetric irreflexive relation of complementarity — the obtained chain is a modified de Bruijn sequence with shifted windows.
References
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Journal ArticleDOI
1-Tuple DNA Sequencing: Computer Analysis
TL;DR: It is shown that the biochemical problems connected with the loss of information about the l-tuple DNA composition during hybridization are not crucial and can be overcome by finding the maximal flow of minimal cost in the special graph.
Journal ArticleDOI
Combinatorial algorithms for DNA sequence assembly
John Kececioglu,Eugene W. Myers +1 more
TL;DR: A four-phase approach based on rigorous design criteria is presented, and has been found to be very accurate in practice and can accommodate high sequencing error rates.