Related papers: The TAG array of a multiple sequence alignment
A parameterized string (p-string) is a string over an alphabet $(\Sigma_{s} \cup \Sigma_{p})$, where $\Sigma_{s}$ and $\Sigma_{p}$ are disjoint alphabets for static symbols (s-symbols) and for parameter symbols (p-symbols), respectively.…
Identifying phenotypes plays an important role in furthering our understanding of disease biology through practical applications within healthcare and the life sciences. The challenge of dealing with the complexities and noise within…
Pangenomes serve as a framework for joint analysis of genomes of related organisms. Several pangenome models were proposed, offering different functionalities, applications provided by available tools, their efficiency etc. Among them, two…
The Burrows-Wheeler transform (BWT) is integral to the FM-index, which is used extensively in text compression, indexing, pattern search, and bioinformatic problems as de novo assembly and read alignment. Thus, efficient construction of the…
Parameterized strings are a generalization of strings in that their characters are drawn from two different alphabets, where one is considered to be the alphabet of static characters and the other to be the alphabet of parameter characters.…
The Burrows-Wheeler Transform (BWT) moves characters with similar contexts in a text together, where a character's context consists of the characters immediately following it. We say that a property has contextual locality if characters…
The advent of "next-generation" DNA sequencing (NGS) technologies has meant that collections of hundreds of millions of DNA sequences are now commonplace in bioinformatics. Knowing the longest common prefix array (LCP) of such a collection…
Combined inference for heterogeneous high-dimensional data is critical in modern biology, where clinical and various kinds of molecular data may be available from a single study. Classical genetic association studies regress a single…
High-throughput sequencing technologies have led to explosive growth of genomic databases; one of which will soon reach hundreds of terabytes. For many applications we want to build and store indexes of these databases but constructing such…
In a \emph{weighted sequence}, for every position of the sequence and every letter of the alphabet a probability of occurrence of this letter at this position is specified. Weighted sequences are commonly used to represent imprecise or…
Sequence alignment is common nowadays as it is used in many fields to determine how closely two sequences are related and at times to see how little they differ. In computational biology / Bioinformatics, there are many algorithms developed…
Genome sequence analysis plays a pivotal role in enabling many medical and scientific advancements in personalized medicine, outbreak tracing, and forensics. However, the analysis of genome sequencing data is currently bottlenecked by the…
Taking advantages of high-throughput genotyping technology of single nucleotide polymorphism (SNP), large genome-wide association studies (GWASs) have been considered as the promise to unravel the complex relationships between genotypes and…
Constructing the Burrows-Wheeler transform (BWT) for long strings poses significant challenges regarding construction time and memory usage. We use a prefix of the suffix array to partition a long string into shorter substrings, thereby…
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…
By using the Jensen-Shannon divergence, genomic DNA can be divided into compositionally distinct domains through a standard recursive segmentation procedure. Each domain, while significantly different from its neighbours, may however share…
An interesting and frequent type of multi-word expression (MWE) is the headless MWE, for which there are no true internal syntactic dominance relations; examples include many named entities ("Wells Fargo") and dates ("July 5, 2020") as well…
Indexing very large collections of strings, such as those produced by the widespread next generation sequencing technologies, heavily relies on multistring generalization of the Burrows-Wheeler Transform (BWT): large requirements of…
The connectome, a map of the structural and/or functional connections in the brain, provides a complex representation of the neurobiological phenotypes on which it supervenes. This information-rich data modality has the potential to…
Genome-wide association study (GWAS) tests single nucleotide polymorphism (SNP) markers across the genome to localize the underlying causal variant of a trait. Because causal variants are seldom observed directly, a surrogate model based on…