AbstractMotivation. Estimating mutation rates between evolutionarily related sequences is a central problem in molecular evolution. Due to the rapid expans

Randomness is a powerful tool in the design and analysis of algorithms and data structures for nucleotide sequence data. Nucleotide sequences are not themselves random but are often randomized using hash functions. Despite their widespread use in genomics, there is no comprehensive review of the types of hash functions used and their various applications. In this survey intended for bioinformatic methods developers, we divide hash functions into four categories: scattering hash functions, permutations, minimum perfect hash functions, and locality-sensitive hash functions. For each category, we provide examples of both general-use hash functions that have been applied in nucleotide sequence analysis and hash functions that have been designed specifically for nucleotide sequence analysis. We highlight their salient properties, commonalities, differences, and application areas.

Matematiska institutionen består av cirka 120 forskare, lärare och administrativ personal och är organiserad i tre huvudsakliga avdelningar: Matematik, Matematisk statistik och Beräkningsmatematik

An easy-to-use, flexible website template for labs, with automatic citations, GitHub tag imports, pre-built components, and more.

Probabilistic membership filters support fast approximate membership queries with a controlled false-positive probability $\varepsilon$ and are widely used across storage, analytics, networking, and b...

Workshop Data Structures in Bioinformatics

The Azrieli Fellows Program is an elite group of academics who cultivate a network of leading professionals in Israel and around the world.

MetaGraph enables scalable indexing of large sets of DNA, RNA or protein sequences using annotated de Bruijn graphs.

Job Description Summary Organization's Summary Statement: The postdoctoral research associate is responsible for developing novel computational methodology for high-throughput sequence genomics tasks,...

Videos on : (a) the Burrows-Wheeler Transform (BWT), (b) the FM Index, which uses the BWT to construct a full-text index, (c) Wheeler graphs, (d) r-index, an...

We introduce Mapping-friendly Sequence Reduction (MSR) sketches, a sketching method for high-fidelity (HiFi) long reads, and Alice, an assembler that operates directly on these sketches. MSR produces ...

Using sequencing and haplotype-resolved assembly of 65 diverse human genomes, complex regions including the major histocompatibility complex and centromeres are analysed.

We introduce FAMSA2, an algorithm that produces high-accuracy multiple protein sequence alignments with unprecedented speed. Across structural, phylogenetic, and functional benchmarks, FAMSA2 matches ...

AbstractSummary. Biological sequence analysis often relies on reference genomes, but producing accurate assemblies remains a challenge. As a result, de nov

AbstractMotivation. Recent advances in high-throughput and third-generation sequencing technologies have created significant challenges in storing and mana

Abstract. Viral subgenomic RNA (sgRNA) plays a major role in SARS-COV2’s replication, pathogenicity, and evolution. Recent sequencing protocols, such as th

The exponential growth of global sequencing data repositories presents both analytical challenges and opportunities. While k - mer-based indexing has improved scalability over traditional alignment fo...

WABI Conference on Algorithms in Bioinformatics

Quality Control downstream of alevin-fry / simpleaf - COMBINE-lab/QCatch

Pangenome graphs represent the genomic variation by encoding multiple haplotypes within a unified graph structure. However, efficient and lossless indexing of such structures remains challenging due t...

AbstractMotivation. Long-read sequencing techniques can sequence transcripts from end to end, greatly improving our ability to study the transcription proc

WABI Conference on Algorithms in Bioinformatics