Related papers: Comparative Assembly Hubs: Web Accessible Browsers…
The UCSC Genome Browser is a popular tool for the exploration and analysis of reference genomes. Mirrors of the UCSC Genome Browser and its contents exist at multiple geographic locations, and this mirror procedure has been modified to…
The immense increase in the generation of genomic scale data poses an unmet analytical challenge, due to a lack of established methodology with the required flexibility and power. We propose a first principled approach to statistical…
With small-scale quantum processors transitioning from experimental physics labs to industrial products, these processors allow us to efficiently compute important algorithms in various fields. In this paper, we propose a quantum algorithm…
De novo genome assembly is challenging in highly repetitive regions; however, reference-guided assemblers often suffer from bias. We propose a framework for pangenome-guided sequence assembly, which can resolve short-read data in complex…
With current hardware and software, a standard computer can now hold in RAM an index for approximate pattern matching on about half a dozen human genomes. Sequencing technologies have improved so quickly, however, that scientists will soon…
CSA is a web server for the comprehensive comparison of pairwise protein structure alignments. Its exact alignment engine computes either optimal, top-scoring alignments or heuristic alignments with quality guarantee for the inter-residue…
Genetic information is encoded in a linear sequence of nucleotides, represented by letters ranging from thousands to billions. Mutations refer to changes in the DNA or RNA nucleotide sequence. Thus, mutation detection is vital in all areas…
Genome assembly from the high-throughput sequencing (HTS) reads is a fundamental yet challenging computational problem. An intrinsic challenge is the uncertainty caused by the widespread repetitive elements. Here we get around the…
Alignment of large genomic sequences is a fundamental task in computational genome analysis. Most methods for genomic alignment use high-scoring local alignments as {\em anchor points} to reduce the search space of the alignment procedure.…
Computational complexity is a key limitation of genomic analyses. Thus, over the last 30 years, researchers have proposed numerous fast heuristic methods that provide computational relief. Comparing genomic sequences is one of the most…
DNA technologies have evolved significantly in the past years enabling the sequencing of a large number of genomes in a short time. Nevertheless, the underlying computational problem is hard, and many technical factors and limitations…
Motivation: Genomic data analyses such as Genome-Wide Association Studies (GWAS) or Hi-C studies are often faced with the problem of partitioning chromosomes into successive regions based on a similarity matrix of high-resolution,…
Currently, third-generation sequencing techniques, which allow to obtain much longer DNA reads compared to the next-generation sequencing technologies, are becoming more and more popular. There are many possibilities to combine data from…
In genomics, pattern matching against a sequence of nucleotides plays a pivotal role for DNA sequence alignment and comparing genomes. This helps tackling some diseases, such as cancer in humans. The complexity of searching biological…
The effective visualization of genomic data is crucial for exploring and interpreting complex relationships within and across genes and genomes. Despite advances in developing dedicated bioinformatics software, common visualization tools…
This preprint presents a web app (essentially a web page-based program) with which two or more users (peers) can view and handle 3D molecular structures in a concurrent, interactive way through their web browsers. This means they can share…
The biological significance of genomic features is often context-dependent. We present CruzDB, a fast and intuitive programmatic interface to the UCSC genome browser that facilitates integrative analyses of diverse local and remotely hosted…
Data commons collate data with cloud computing infrastructure and commonly used software services, tools and applications to create biomedical resources for the large-scale management, analysis, harmonization, and sharing of biomedical…
Identification and alignment of three-dimensional folding of proteins may yield useful information about relationships too remote to be detected by conventional methods, such as sequence comparison, and may potentially lead to prediction of…
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…