Related papers: Efficient Construction of a Complete Index for Pan…
DNA sequencing, especially of microbial genomes and metagenomes, has been at the core of recent research advances in large-scale comparative genomics. The data deluge has resulted in exponential growth in genomic datasets over the past…
The Burrows-Wheeler transform (BWT) is a well studied text transformation widely used in data compression and text indexing. The BWT of two strings can also provide similarity measures between them, based on the observation that the more…
We propose a new technique for creating a space-efficient index for large repetitive text collections, such as pangenomic databases containing sequences of many individuals from the same species. We combine two recent techniques from this…
Genomics is the foundation of precision medicine, global food security and virus surveillance. Exact-match is one of the most essential operations widely used in almost every step of genomics such as alignment, assembly, annotation, and…
The Burrows-Wheeler transform (BWT) is a permutation whose applications are prevalent in data compression and text indexing. The bijective BWT (BBWT) is a bijective variant of it. Although it is known that the BWT can be constructed in…
Pairwise alignment of DNA sequencing data is a ubiquitous task in bioinformatics and typically represents a heavy computational burden. State-of-the-art approaches to speed up this task use hashing to identify short segments (k-mers) that…
The recent introduction of learned indexes has shaken the foundations of the decades-old field of indexing data structures. Combining, or even replacing, classic design elements such as B-tree nodes with machine learning models has proven…
Cartesian tree matching is a form of generalized pattern matching where a substring of the text matches with the pattern if they share the same Cartesian tree. This form of matching finds application for time series of stock prices and can…
Motivation: The availability of thousands of invidual genomes of one species should boost rapid progress in personalized medicine or understanding of the interaction between genotype and phenotype, to name a few applications. A key…
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…
A new array based data structure named black-white array (BWA) is introduced as an effective and efficient alternative to the list or tree based data structures for dynamic data set. It consists of two sub-arrays, one white and one black of…
Text indexing is a fundamental and well-studied problem. Classic solutions either replace the original text with a compressed representation, e.g., the FM-index and its variants, or keep it uncompressed but attach some redundancy - an index…
There are various approaches to exploiting "hidden structure" in instances of hard combinatorial problems to allow faster algorithms than for general unstructured or random instances. For SAT and its counting version #SAT, hidden structure…
We study the problem of local alignment, which is finding pairs of similar subsequences with gaps. The problem exists in biosequence databases. BLAST is a typical software for finding local alignment based on heuristic, but could miss…
In this paper we describe algorithms for computing the BWT and for building (compressed) indexes in external memory. The innovative feature of our algorithms is that they are lightweight in the sense that, for an input of size $n$, they use…
In this paper, we consider the problem of compressing a trie while supporting the powerful \emph{locate} queries: to return the pre-order identifiers of all nodes reached by a path labeled with a given query pattern. Our result builds on…
The Burrows-Wheeler Transform (BWT) is an efficient invertible text transformation algorithm with the properties of tending to group identical characters together in a run, and enabling search of the text. This transformation has extensive…
Converting a set of sequencing reads into a lossless compact data structure that encodes all the relevant biological information is a major challenge. The classical approaches are to build the string graph or the de Bruijn graph. Each has…
A recent paradigm shift in bioinformatics from a single reference genome to a pangenome brought with it several graph structures. These graph structures must implement operations, such as efficient construction from multiple genomes and…
Innovations in Next-Generation Sequencing are enabling generation of DNA sequence data at ever faster rates and at very low cost. Large sequencing centers typically employ hundreds of such systems. Such high-throughput and low-cost…