相关论文: Understanding Long-range Correlations in DNA Seque…
When it is viewed at the scale of a base pair, DNA appears as a nonlinear lattice. Modelling its properties is a fascinating goal. The detailed experiments that can be performed on this system impose constraints on the models and can be…
This paper presents a probabilistic approach for DNA sequence analysis. A DNA sequence consists of an arrangement of the four nucleotides A, C, T and G and different representation schemes are presented according to a probability measure…
Motivation: DNA data is transcribed into single-stranded RNA, which folds into specific molecular structures. In this paper we pose the question to what extent sequence- and structure-information correlate. We view this correlation as…
In array-based DNA synthesis, multiple strands of DNA are synthesized in parallel to reduce the time cost from the sum of their lengths to the length their shortest common supersequences. To maximize the amount of information that can be…
A new set of DNA base-nucleic acid codes and their hypercomplex number representation have been introduced for taking the probability of each nucleotide into full account. A new scoring system has been proposed to suit the hypercomplex…
In molecular phylogeny, relationships among organisms are reconstructed using DNA or protein sequences and are displayed as trees. A linear increase in the number of sequences results in an exponential increase of possible trees. Thus,…
Background: Duplication of genes is important for evolution of molecular networks. Many authors have therefore considered gene duplication as a driving force in shaping the topology of molecular networks. In particular it has been noted…
Periodic patterns play the important regulatory and structural roles in genomic DNA sequences. Commonly, the underlying periodicities should be understood in a broad statistical sense, since the corresponding periodic patterns have been…
Various approaches to alignment-free sequence comparison are based on the length of exact or inexact word matches between two input sequences. Haubold {\em et al.} (2009) showed how the average number of substitutions between two DNA…
The characterization of the long-range order and fractal properties of DNA sequences has proved a difficult though highly rewarding task due mainly to the mosaic character of DNA consisting of many interwoven patches of various lengths with…
Gene duplication is a fundamental evolutionary mechanism that contributes to biological complexity and diversity (Fortna et al., 2004). Traditionally, research has focused on the duplication of gene sequences (Zhang, 1914). However,…
The reconstruction of phylogenies from DNA or protein sequences is a major task of computational evolutionary biology. Common phenomena, notably variations in mutation rates across genomes and incongruences between gene lineage histories,…
At the core of high throughput DNA sequencing platforms lies a bio-physical surface process that results in a random geometry of clusters of homogenous short DNA fragments typically hundreds of base pairs long - bridge amplification. The…
Molecular recognition between two double stranded (ds) DNA with homologous sequences may not seem compatible with the B-DNA structure because the sequence information is hidden when it is used for joining the two strands. Nevertheless, it…
We consider force-induced unzipping transition for a heterogeneous DNA model with a correlated base-sequence. Both finite-range and long-range correlated situations are considered. It is shown that finite-range correlations increase…
Recent studies have revealed that for the majority of species the length distributions of duplicated sequences in natural DNA follow a power-law tail. We study duplication-mutation models for processes in natural DNA sequences and the…
Biological cells replicate their genomes in a well-planned manner. The DNA replication program of an organism determines the timing at which different genomic regions are replicated, with fundamental consequences for cell homeostasis and…
Complex systems with tightly coadapted parts frequently appear in living systems and are difficult to account for through Darwinian evolution, that is random variation and natural selection, if the constituent parts are independently coded…
Symbolic sequences such as written language and genomic DNA display characteristic frequency distributions and long-range correlations extending over many symbols. In language, this takes the form of Zipf's law for word frequencies together…
We introduce a model of DNA sequence evolution which can account for biases in mutation rates that depend on the identity of the neighboring bases. An analytic solution for this class of non-equilibrium models is developed by adopting…