SUMMARY: The Integrated Database of Small Molecules (IDSM) integrates data from small-molecule datasets, making them accessible through the SPARQL query language. Its unique feature is the ability to search for compounds through SPARQL based on their molecular structure. We extended IDSM to enable mass spectra databases to be integrated and searched for based on mass spectrum similarity. As sources of mass spectra, we employed the MassBank of North America database and the In Silico Spectral Database of natural products. AVAILABILITY AND IMPLEMENTATION: The extension is an integral part of IDSM, which is available at https://idsm.elixir-czech.cz. The manual and usage examples are available at https://idsm.elixir-czech.cz/docs/ms. The source codes of all IDSM parts are available under open-source licences at https://github.com/idsm-src.

BACKGROUND: The specific recognition of a DNA locus by a given transcription factor is a widely studied issue. It is generally agreed that the recognition can be influenced not only by the binding motif but by the larger context of the binding site. In this work, we present a novel heuristic algorithm that can reconstruct the unique binding sites captured in a sequencing experiment without using the reference genome. RESULTS: We present PAPerFly, the Partial Assembly-based Peak Finder, a tool for the binding site and binding context reconstruction from the sequencing data without any prior knowledge. This tool operates without the need to know the reference genome of the respective organism. We employ algorithmic approaches that are used during genome assembly. The proposed algorithm constructs a de Bruijn graph from the sequencing data. Based on this graph, sequences and their enrichment are reconstructed using a novel heuristic algorithm. The reconstructed sequences are aligned and the peaks in the sequence enrichment are identified. Our approach was tested by processing several ChIP-seq experiments available in the ENCODE database and comparing the results of Paperfly and standard methods. CONCLUSIONS: We show that PAPerFly, an algorithm tailored for experiment analysis without the reference genome, yields better results than an aggregation of ChIP-seq agnostic tools. Our tool is freely available at https://github.com/Caeph/paperfly/ or on Zenodo ( https://doi.org/10.5281/zenodo.7116424 ).

SUMMARY: ShinySOM offers a user-friendly interface for reproducible, high-throughput analysis of high-dimensional flow and mass cytometry data guided by self-organizing maps. The software implements a FlowSOM-style workflow, with improvements in performance, visualizations and data dissection possibilities. The outputs of the analysis include precise statistical information about the dissected samples, and R-compatible metadata useful for the batch processing of large sample volumes. AVAILABILITY AND IMPLEMENTATION: ShinySOM is free and open-source, available online at gitlab.com/exaexa/ShinySOM. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Summary: Amino acid residues showing above background levels of conservation are often indicative of functionally significant regions within a protein. Understanding how the sequence conservation profile relates in space requires projection onto a protein structure, a potentially time-consuming process. 3DPatch is a web application that streamlines this task by automatically generating multiple sequence alignments (where appropriate) and finding structural homologs, presenting the user with a choice of structures matching their query, annotated with residue conservation scores in a matter of seconds. Availability and implementation: 3DPatch is written in JavaScript and is freely available at http://www.skylign.org/3DPatch/. Mozilla Firefox, Google Chrome, and Safari web browsers are supported. Source code is available under MIT license at https://github.com/davidjakubec/3DPatch. Supplementary information: Supplementary data are available at Bioinformatics online.