Services: software tools

Comprehensive resource of human phosphosites within their full context.

Annotation of secondary structure elements in proteins.

A tool for semantic analysis of microarray data based on a collection of workflow components for Orange4WS

Web server for RNA structure comparison.

SIAMCAT is a modular framework for the statistical inference of associations between microbial communities and host phenotypes, such as disease states in clinical case-control studies. SIAMCAT is based on LASSO models, which offer distinctive advantages for model interpretation and microbial biomarker selection and avoid overfitting issues that can arise in naive combinations of feature selection and cross-validation. Part of the Microbiome Analysis Toolbox. 

Data Analysis service for ribosomal RNA

Web application to compare multiple protein structural motifs.

slalom is a scalable modelling framework for single-cell RNA-seq data that uses gene set annotations to dissect single-cell transcriptome heterogeneity, thereby allowing identification of biological drivers of cell-to-cell variability and model confounding factors.

SMART (Simple Modular Architecture Research Tool) is a web resource providing simple identification and extensive annotation of protein domains via sequence homology searches. It contains manually curated models for more than 1,200 protein domains. In its ‘Genomic’ mode, it annotates proteins from completely sequenced genomes of 2,031 species as a basis for their functional annotation. It provides flexible tools to visually explore protein domain architectures across sequences and organisms. Part of the Human Omics Analysis Toolbox. 

SNPmasker is a program to mask all SNPs in given sequence using information of dbSNP. Additionally it is possible to mask all non-unique words using GenomeMasker module.

Analysis workflow for plant sRNA sequencing data.

SweeD is a high-performance computing software that detects the site of the beneficial mutation, using the Site Frequency Spectrum. It can analyze whole genome data of thousands of individuals in a few hours.

SWISS-MODEL is a fully automated service for protein structure homology modelling. It provides a personal web based workspace for interactive modelling, storing project data and visualizing results online. 

SwissDrugDesign provides a collection of web-based tools covering all aspects of computer-aided drug design.

SymCurv is a computational ab initio method for nucleosome positioning prediction. It is based on the structural property of natural nucleosome forming sequences, to be symmetrically curved around a local minimum of curvature.

Database of protein association networks representing a broad scala of biological associations between pairs of proteins that go beyond  direct protein interactions

TAndem REpeat ANalyzer -TAREAN – is a computational pipeline for unsupervised identification of satellite repeats from unassembled sequence reads. The pipeline uses low-pass whole genome sequence reads and performs their graph-based clustering. Resulting clusters, representing all types of repeats, are then examined for the presence of circular structures and putative satellite repeats are reported.

Web tool for the prediction of T-cell receptor epitope recognition.

Contains tools for the functional classification of PLP-dependent enzymes in predicted protein sequences.

A web-based system for finding and testing relations between high-throughput sequencing and/or other genomic datasets (tracks), making use of statistical hypothesis testing and other advanced methodology.

Based on ICGC PanCancer infrastructure for organising and processing NGS data using workflow plugins including:  

• Workflow Plug-Ins - provide pipelines for the most common NGS processing tasks, including alignment (WES, WGS, WGBS, RNA-seq), quality control and variant calling (SNV, indel, CNV, SV).
• Cloud/HPC - IT Infrastructure for de.NBI users based on ICGC and TCGA PanCancer technology
• OTP - "One Touch Pipeline" is a comprehensive framework for NGS project organization and processing.
• Roddy - a framework for large scale NGS processing pipelines on Petabyte scale for the management of workflows in the Pan-Cancer Analysis of Whole Genomes (PCAWG) project.

The OpenMS Proteomics Pipeline making a range of tools available, including MetaProSIP and TOPPview. 

Visualising own data through OpenMS tools, including spectra, chromatograms, 2D LC-MS data and annotations. 

Template-based RNA secondary structure visualization.

Trimmomatic is a flexible read trimming tool for NGS data.

Platform for metaproteomics data analysis with a focus on interactive data visualizations

UniProt Related Documents (UniReD): assisting wet lab biologists
in their quest on finding novel counterparts in a protein network

Tools for processing the topology and structure of transmembrane proteins

• A. Constrained Consensus TOPology prediction server (CCTOP) 
• B. Transmembrane helices and protein topology prediction (HMMTOP),
• C. Detection of transmembrane regions (TMDET)
• D. Transmembrane proteins’ membrane segments folding recognizing (TmFoldWeb)

Public Galaxy instance enabling reproducible data analysis through workflows

V-pipe is the bioinformatics pipeline that integrates various open-source software packages for assessing viral genetic diversity from next-generation sequencing (NGS) data derived from intra-host virus populations. V-pipe enables reliable and comparable viral pathogen genomics and epidemiological studies and facilitates clinical diagnostics of viruses.