Services: Software Tools

E-CRISP is a computational tool to design and evaluate guide RNAs for use with CRISPR/Cas9. The web application uses fast algorithms to identify target sequences for use with mediated genome editing. E-CRISP analyzes target specificity of the putative designs and assesses their genomic context (e.g. exons, transcripts, CpG islands). The design process incorporates different parameters of how CRISPR constructs can be used in experimental applications, such as knock-out and tagging experiments. E-CRISP can design guide RNAs for genomes of more than 30 organisms.

easyFRAP-web is a versatile web-based tool that assists quantitative and qualitative analysis of fluorescence recovery after photobleaching (FRAP) data

R/Bioconductor package that provides general purpose functionality for the reading, writing, processing and analysis of images. In the context of high-throughput microscopy based cellular assays, EBImage offers tools to transform the images, segment cells and extract quantitative cellular descriptors. Part of the Human Omics Analysis Toolbox

Using BLAST score analysis to identify orthologous genes in large groups of related genomes

Easily interpretable electron density score for individual atoms. 

The ELIXIR-GR Cloud Infrastructure (EG-CI) is a Cloud infrastructure being developed to support a broad spectrum of bioinformatic services provided to the community of life scientists in Greece and other ELIXIR Members.

 An API aiming to enable the search of genomic variants and associated information without jeopardising the privacy of the dataset.

A Jekyll theme designed to support easy deployment of documentation websites, as well as more complex sites requiring a central tool table and linking towards ELIXIR resources.

Tools to submit sequencing data to the European Nucleotide Archive (ENA). The tools feature a single-step submission process, a graphical user interface, tabular-formatted metadata and the possibility to remove human reads prior to submission.

EnrichedHeatmaps is an R package which visualizes the enrichment of genomic signals on specific target region

Enterotypes are densely populated regions in a high-dimensional space of microbiome community composition, by which human individuals can be stratified. Computational methods to detect and characterise enterotypes in any dataset, either to reproduce previous reports or determine enterotypes in new studies, are provided and explained. Part of the Microbiome Analysis Toolbox. 

A web tool for easy construction and quick testing of kinetic models of enzyme catalyzed reactions. Automatic assembly and calibration of models of enzymatic reactions based on ordinary differential equations.

EnzymeMiner identifies putative members of enzyme families or subfamilies and facilitates the selection of promising targets for experimental characterization. Two key selection criteria are (i) the predicted solubility and (ii) the sequence identities visualised using an interactive sequence similarity network. The search query can be a sequence from the Swiss-Prot database or a custom sequence with a custom description of essential residues. The output is an interactive selection table containing annotated identified sequences.

Online platform for comparing methylation data

Efficient detection of protein disorder: web server and tool for protein region detection which are thought to contain no structural content.

For analysis of high-throughput sequencing incorporating many tools, training, literature and guides

eggNOG is a database of nested orthologous gene groups (NOGs) infered using unsupervised clustering applied to >2,000 complete genomes followed by comprehensive characterization and analysis of the resulting gene families. eggNOG provides orthologous group assignments at >100 different taxonomic levels as well as multiple sequence alignments, maximum-likelihood trees and broad functional annotations for each group accessible via a web interface or through bulk download. Part of the Microbiome Analysis Toolbox.

Allows the easy comparison of publicly available data from the main Protein-Protein Interaction (PPI) databases for the same and distinct species.

SIB's resource portal with access to all major tools and databases provided by different SIB groups and external partners. Specific query features allow interacting with many resources at the same time. 

FAIDARE is a portal developed by ELIXIR-FR as an asset of the ELIXIR Plant Science community. FAIDARE enables data discovery through federations of distant Plant informations systems that have set up a standardized Restful API, the BrAPI. FAIDARE currently allows to do detailed searches of accessions and phenotyping data.

An information and educational resource of inter-related data standards, databases and policies. 

This API allows validating JSON contents following JSON Schema defined at https://github.com/fairtracks/fairtracks_standard/

FireProt is a web server for an automated design of thermostable mutants. The design of thermostable mutants is based on the integration of structural and evolutionary information obtained from several bioinformatics databases and computational tools.

FireProt-ASR is a web server for an automated calculation of ancestral sequences. Fireprot-ASR allows you to perform ancestral sequence reconstruction starting from a single protein sequence. The pipeline first compiles a dataset of catalytically similar protein sequences, aligns them, construct their phylogenetic tree, and then reconstruct ancestral nodes. It also allows user to input their own data and start from a different point in the pipeline.

OpenMS tool for Top-Down MS data deconvolution.

FLASHIda is an intelligent online data acquisition algorithm for top-down proteomics (TDP) that ensures the real-time selection of high-quality precursors of diverse proteoforms. 

FLASHQuant performs MS1-level label-free quantification data analysis in top-down proteomics, with an automatic overlapping signal resolution method.

An online access to a series of RNA research tools for sequence-structure alignments, clustering, interaction prediction, identification of homologs etc

Web application for the integrative and combined analysis and visualization of multi-level omics data. (Replaced ProMeTra)

g:Profiler is a bioinformatics toolkit for characterising and manipulating gene lists of high-throughput genomic data.