Related papers: Estimating phylogenetic distances between genomic …
A new family of compound Poisson distribution functions from statistical linguistic is used to study the n-tuples and nucleotide composition features of DNA sequences. The relative frequency distribution of the 6-tuples and 7- tuples…
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…
Understanding the mutational history of tumor cells is a critical endeavor in unraveling the mechanisms underlying cancer. Since the modeling of tumor cell evolution employs labeled trees, researchers are motivated to develop different…
The nature of the alignment with gaps corresponding to a longest common subsequence (LCS) of two independent iid random sequences drawn from a finite alphabet is investigated. It is shown that such an optimal alignment typically matches…
We obtain an explicit formula for the variance of the number of $k$-peaks in a uniformly random permutation. This is then used to obtain an asymptotic formula for the variance of the length of longest $k$-alternating subsequence in random…
String matching algorithm plays the vital role in the Computational Biology. The functional and structural relationship of the biological sequence is determined by similarities on that sequence. For that, the researcher is supposed to aware…
The main statistical distributions applicable to the analysis of genome architecture and genome tracks are briefly discussed and critically assessed. Although the observed features in distributions of element lengths can be equally well…
Sequencing by synthesis is the underlying technology for many next-generation DNA sequencing platforms. We developed a new model, the fixed flow cycle model, to derive the distributions of sequence length for a given number of flow cycles…
We present a new streaming algorithm for the $k$-Mismatch problem, one of the most basic problems in pattern matching. Given a pattern and a text, the task is to find all substrings of the text that are at the Hamming distance at most $k$…
Modelling semantic similarity plays a fundamental role in lexical semantic applications. A natural way of calculating semantic similarity is to access handcrafted semantic networks, but similarity prediction can also be anticipated in a…
Mutual correlation between segments of DNA or protein sequences can be detected by Smith-Waterman local alignments. We present a statistical analysis of alignment of such sequences, based on a recent scaling theory. A new fidelity measure…
We consider the problem of identifying tandem scattered subsequences within a string. Our algorithm identifies a longest subsequence which occurs twice without overlap in a string. This algorithm is based on the Hunt-Szymanski algorithm,…
Accurate estimation of evolutionary distances between taxa is important for many phylogenetic reconstruction methods. In the case of bacteria, distances can be estimated using a range of different evolutionary models, from single nucleotide…
Enormous volumes of short reads data from next-generation sequencing (NGS) technologies have posed new challenges to the area of genomic sequence comparison. The multiple sequence alignment approach is hardly applicable to NGS data due to…
Next Generation Sequencing (NGS) technologies generate large amounts of short read data for many different organisms. The fact that NGS reads are generally short makes it challenging to assemble the reads and reconstruct the original genome…
The utility of DNA sequence substrings (k-mers) in alignment-free phylogenetic classification, including that of bacteria and viruses, is increasingly recognized. However, its biological basis eludes many twenty-first century practitioners.…
Distance-based approaches in phylogenetics such as Neighbor-Joining are a fast and popular approach for building trees. These methods take pairs of sequences from them construct a value that, in expectation, is additive under a stochastic…
Sequence segmentation is a well-studied problem, where given a sequence of elements, an integer K, and some measure of homogeneity, the task is to split the sequence into K contiguous segments that are maximally homogeneous. A classic…
The statistical properties of local alignment algorithms with gaps are analyzed theoretically for uncorrelated and correlated DNA sequences. In the vicinity of the log-linear phase transition, the statistics of alignment with gaps is shown…
We present analytical results for the distribution of shortest path lengths between random pairs of nodes in configuration model networks. The results, which are based on recursion equations, are shown to be in good agreement with numerical…