Related papers: Comparing DNA sequence collections by direct compa…
Recently, Holt and McMillan [Bionformatics 2014, ACM-BCB 2014] have proposed a simple and elegant algorithm to merge the Burrows-Wheeler transforms of a family of strings. In this paper we show that the H&M algorithm can be improved so…
The task of accumulating a portion of a list of values, whose values may be updated at any time, is widely used throughout various applications in computer science. While it is trivial to accomplish this task without any constraints,…
In a distributed information application an encoder compresses an arbitrary vector while a similar reference vector is available to the decoder as side information. For the Hamming-distance similarity measure, and when guaranteed perfect…
The longest common prefix array is a very advantageous data structure that, combined with the suffix array and the Burrows-Wheeler transform, allows to efficiently compute some combinatorial properties of a string useful in several…
Genome assembly using high throughput data with short reads, arguably, remains an unresolvable task in repetitive genomes, since when the length of a repeat exceeds the read length, it becomes difficult to unambiguously connect the flanking…
JSON Lines (JSONL) is widely used for managing large collections of semi-structured data, ranging from large language model (LLM) prompts to chemical compound records and geospatial datasets. A key operation is substructure search, which…
Advances in DNA sequencing mean databases of thousands of human genomes will soon be commonplace. In this paper we introduce a simple technique for reducing the size of conventional indexes on such highly repetitive texts. Given upper…
We first review how we can store a run-length compressed suffix array (RLCSA) for a text $T$ of length $n$ over an alphabet of size $\sigma$ whose Burrows-Wheeler Transform (BWT) consists of $r$ runs in $O \left( \rule{0ex}{2ex} r \log (n /…
Wavelets have emerged as a cutting edge technology in a number of fields. Concrete results of their application in Image and Signal processing suggest that wavelets can be effectively applied to Natural Language Processing (NLP) tasks that…
Pedigree GWAS (Option 29) in the current version of the Mendel software is an optimized subroutine for performing large scale genome-wide QTL analysis. This analysis (a) works for random sample data, pedigree data, or a mix of both, (b) is…
Assessing the correctness of genome assemblies is an important step in any genome project. Several methods exist, but most are computationally intensive and, in some cases, inappropriate. Here I present baa.pl, a fast and easy-to-use…
In recent years, pangenomes received increasing attention from the scientific community for their ability to incorporate population variation information and alleviate reference genome bias. Maximal Exact Matches (MEMs) and Maximal Unique…
Various methods have been developed to analyze the association between organisms and their genomic sequences. Among them, sequence alignment is the most frequently used for comparative analysis of biological genomes. However, the…
Drug development is a very costly and lengthy process, while repositioned or repurposed drugs could be brought into clinical practice within a shorter time-frame and at a much reduced cost. The past decade has observed a massive growth in…
The Bag-of-Words (BoW) representation is well applied to recent state-of-the-art image retrieval works. Typically, multiple vocabularies are generated to correct quantization artifacts and improve recall. However, this routine is corrupted…
Scoring DNA sequences against Position Weight Matrices (PWMs) is a widely adopted method to identify putative transcription factor binding sites. While common bioinformatics tools produce scores that can reflect the binding strength between…
In the last decade a number of algorithms and associated software have been developed to align next generation sequencing (NGS) reads with relevant reference genomes. The accuracy of these programs may vary significantly, especially when…
Wavelet trees are widely used in the representation of sequences, permutations, text collections, binary relations, discrete points, and other succinct data structures. We show, however, that this still falls short of exploiting all of the…
Set similarity join, as well as the corresponding indexing problem set similarity search, are fundamental primitives for managing noisy or uncertain data. For example, these primitives can be used in data cleaning to identify different…
In this paper we study the number $r_{bwt}$ of equal-letter runs produced by the Burrows-Wheeler transform ($BWT$) when it is applied to purely morphic finite words, which are words generated by iterating prolongable morphisms. Such a…