Published in Bioinformatics (Oxford, England)
Next-generation sequencing is rapidly improving diagnostic rates in rare Mendelian diseases, but even with whole genome or whole exome sequencing, the majority of cases remain unsolved. Increasingly, RNA sequencing is being used to solve many cases that evade diagnosis through sequencing alone. Specifically, the detection of aberrant splicing in ma...
Published in Bioinformatics (Oxford, England)
A primary problem in high-throughput genomics experiments is finding the most important genes involved in biological processes (e.g. tumor progression). In this applications note, we introduce spathial, an R package for navigating high-dimensional data spaces. spathial implements the Principal Path algorithm, which is a topological method for local...
Published in Bioinformatics (Oxford, England)
Published in Bioinformatics (Oxford, England)
As genomic data becomes more abundant, efficient algorithms and data structures for sequence alignment become increasingly important. The suffix array is a widely used data structure to accelerate alignment, but the binary search algorithm used to query it requires widespread memory accesses, causing a large number of cache misses on large datasets...
Published in Bioinformatics (Oxford, England)
RNA solvent accessibility, similar to protein solvent accessibility, reflects the structural regions that are accessible to solvents or other functional biomolecules, and plays an important role for structural and functional characterization. Unlike protein solvent accessibility, only a few tools are available for predicting RNA solvent accessibili...
Published in Bioinformatics (Oxford, England)
Structured semantic resources, for example, biological knowledge bases (KBs) and ontologies, formally define biological concepts, entities and their semantic relationships, manifested as structured axioms and unstructured texts (e.g., textual definitions). The resources contain accurate expressions of biological reality and have been used by machin...
Published in Bioinformatics (Oxford, England)
SeqEditor is a cross-platform desktop application for the analysis of nucleotide and protein sequences. It is managed through a Graphical User Interface (GIU) and can work either as a graphical sequence browser or as a fasta task manager for multi-fasta files. SeqEditor has been optimized for the management of large sequences, such as contigs, scaf...
Published in Bioinformatics (Oxford, England)
NanoCLUST is an analysis pipeline for classification of amplicon-based full-length 16S rRNA nanopore reads. It is characterized by an unsupervised read clustering step, based on Uniform Manifold Approximation and Projection (UMAP), followed by the construction of a polished read and subsequent Blast classification. Here we demonstrate that NanoCLUS...
Published in Bioinformatics (Oxford, England)
The majority of the proteins in living organisms occur as homo- or hetero-multimeric structures. While there are many tools to predict the structures of single-chain proteins or protein complexes with small ligands, peptide-protein and protein-protein docking is more challenging. In this work, we utilized multiplexed replica exchange MD simulations...
Published in Bioinformatics (Oxford, England)
Hydrogen-Deuterium eXchange coupled to mass spectrometry (HDX) is a powerful tool for the analysis of protein dynamics and interactions. Bottom-up experiments looking at deuterium uptake differences between various conditions are the most common. These produce multidimensional data that can be challenging to depict in a single visual format. Each u...
