Related papers: Agptools: a utility suite for editing genome assem…
Summary: With the rapid development of long-read sequencing technologies, the era of individual complete genomes is approaching. We have developed wgatools, a cross-platform, ultrafast toolkit that supports a range of whole genome alignment…
The GFF3 format is a common, flexible tab-delimited format representing the structure and function of genes or other mapped features (https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md). However, with increasing…
Short-read DNA sequencing instruments can yield over 1e+12 bases per run, typically composed of reads 150 bases long. Despite this high throughput, de novo assembly algorithms have difficulty reconstructing contiguous genome sequences using…
Pathway Tools is a bioinformatics software environment with a broad set of capabilities. The software provides genome-informatics tools such as a genome browser, sequence alignments, a genome-variant analyzer, and comparative-genomics…
Generative Programming (GP) is a computing paradigm allowing automatic creation of entire software families utilizing the configuration of elementary and reusable components. GP can be projected on different technologies, e.g.…
Analyzing a functional genomics experiment, such as ATAC-, ChIP- or RNA-sequencing, requires reference data including a genome assembly and gene annotation. These resources can generally be retrieved from different organizations and in…
Self assembly is a process by which supramolecular species form spontaneously from their components. This process is ubiquitous throughout the life chemistry and is central to biological information processing. It has been predicted that in…
The number of available genomes of prokaryotic organisms is rapidly growing enabling comparative genomics studies. The comparison of genomes of organisms with a common phenotype, habitat or phylogeny often shows that these genomes share…
The objective of this paper is to define an effective strategy for building an ensemble of Genetic Programming (GP) models. Ensemble methods are widely used in machine learning due to their features: they average out biases, they reduce the…
Manually authoring 3D shapes is difficult and time consuming; generative models of 3D shapes offer compelling alternatives. Procedural representations are one such possibility: they offer high-quality and editable results but are difficult…
We have developed PGPG (Pipeline Generator for Programmable GRAPE), a software which generates the low-level design of the pipeline processor and communication software for FPGA-based computing engines (FBCEs). An FBCE typically consists of…
A genome read data set can be quickly and efficiently remapped from one reference to another similar reference (e.g., between two reference versions or two similar species) using a variety of tools, e.g., the commonly-used CrossMap tool.…
Summary: Macromolecular assembly vertebrates essential cellular processes, such as gene regulation and signal transduction. A major challenge for conventional computational methods to study these processes is tackling the exponential…
The de novo assembly of large, complex genomes is a significant challenge with currently available DNA sequencing technology. While many de novo assembly software packages are available, comparatively little attention has been paid to…
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…
Genetic Programming is an evolutionary algorithm that generates computer programs, or mathematical expressions, to solve complex problems. In this Guide, we demonstrate how to use Genetic Programming to develop surrogate models to mitigate…
De novo assembly is the process of reconstructing the genome sequence of an organism from sequencing reads. Genome sequences are essential to biology, and assembly has been a central problem in bioinformatics for four decades. Until…
Genomics is changing our understanding of humans, evolution, diseases, and medicines to name but a few. As sequencing technology is developed collecting DNA sequences takes less time thereby generating more genetic data every day. Today the…
Gene assembly is an intricate biological process that has been studied formally and modeled through string and graph rewriting systems. Recently, a restriction of the general (intramolecular) model, called simple gene assembly, has been…
De novo genome assembly focuses on finding connections between a vast amount of short sequences in order to reconstruct the original genome. The central problem of genome assembly could be described as finding a Hamiltonian path through a…