Related papers: Comparing DNA sequence collections by direct compa…

Mantaci et al. [TCS 2007] defined the eBWT to extend the definition of the BWT to a collection of strings, however, since this introduction, it has been used more generally to describe any BWT of a collection of strings and the fundamental…

We have recently used genetic programming to automatically generate an improved version of Langmead's DNA read alignment tool Bowtie2 Sect.5.3 RN/12/09. We find it runs more than four times faster than the Bioinformatics sequencing tool…

Variation graphs, which represent genetic variation within a population, are replacing sequences as reference genomes. Path indexes are one of the most important tools for working with variation graphs. They generalize text indexes to…

DNA sequence classification requires not only high predictive accuracy but also the ability to uncover latent site interactions, combinatorial regulation, and epistasis-like higher-order dependencies. Although the standard Transformer…

We propose a new model for learning bilingual word representations from non-parallel document-aligned data. Following the recent advances in word representation learning, our model learns dense real-valued word vectors, that is, bilingual…

The tremdendous advances in high-throughput sequencing technologies have made population-scale sequencing as performed in the 1000 Genomes project and the Genome of the Netherlands project possible. Next-generation sequencing has allowed…

DNA sequence alignment involves assigning short DNA reads to the most probable locations on an extensive reference genome. This process is crucial for various genomic analyses, including variant calling, transcriptomics, and epigenomics.…

DNA sequencing technology has advanced to a point where storage is becoming the central bottleneck in the acquisition and mining of more data. Large amounts of data are vital for genomics research, and generic compression tools, while…

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…

Indexing highly repetitive texts - such as genomic databases, software repositories and versioned text collections - has become an important problem since the turn of the millennium. A relevant compressibility measure for repetitive texts…

The sort transform (ST) is a modification of the Burrows-Wheeler transform (BWT). Both transformations map an arbitrary word of length n to a pair consisting of a word of length n and an index between 1 and n. The BWT sorts all rotation…

We introduce a pipeline to easily generate collections of web accessible UCSC genome browsers interrelated by an alignment. Using the alignment, all annotations and the alignment itself can be efficiently viewed with reference to any genome…

In 1994, Burrows and Wheeler developed a data compression algorithm which performs significantly better than Lempel-Ziv based algorithms. Since then, a lot of work has been done in order to improve their algorithm, which is based on a…

We prove that for every integer $n > 0$ and for every alphabet $\Sigma_k$ of size $k \geq 3$, there exists a necklace of length $n$ whose Burrows-Wheeler Transform (BWT) is completely unclustered, i.e., it consists of exactly $n$ runs with…

Alignment-free sequence analysis approaches provide important alternatives over multiple sequence alignment (MSA) in biological sequence analysis because alignment-free approaches have low computation complexity and are not dependent on…

Reference-guided DNA sequencing and alignment is an important process in computational molecular biology. The amount of DNA data grows very fast, and many new genomes are waiting to be sequenced while millions of private genomes need to be…

Genome sequences contain hundreds of millions of DNA base pairs. Finding the degree of similarity between two genomes requires executing a compute-intensive dynamic programming algorithm, such as Smith-Waterman. Traditional von Neumann…

This paper describes a method to efficiently retrieve protein database sequences similar to a query sequence, while allowing for significant numbers of mutations. We call this method SEQR for SEQuence Retrieval. This approach increases the…

Binary relations are commonly used in Computer Science for modeling data. In addition to classical representations using matrices or lists, some compressed data structures have recently been proposed to represent binary relations in compact…

Prior work inspired by compression algorithms has described how the Burrows Wheeler Transform can be used to create a distance measure for bioinformatics problems. We describe issues with this approach that were not widely known, and…