Services: software tools

The Ocean Gene Atlas service provides data mining access to three complementary data objects: gene sequence catalogs (ENA), sample environmental context (PANGAEA), and gene abundances estimates in samples (computed by mapping raw sequence reads onto gene catalogs). User queries are composed of either a sequence (nucleic or protein), or a hidden Markov model derived from a multiple sequence alignment. Homologs of the user query in the gene catalogs are identified using standard sequence similarity search tools (eg BLAST or HMMER), and their read based estimated abundance are displayed in interactive world maps and ecological plots. A phylogenetic tree is also inferred in order to situate the user query within its context of marine environmental homologs as well as known homologs from reference sequences.

OMPdb is a database of beta-barrel outer membrane proteins from Gram-negative bacteria.

Mass Spec. analysis platform

(See also Topp, LFQProfiler & RNPxl, MetaboProfiler) 

OpenMS tool for the study of Protein-Protein interactions.

Open source software environment for development of biomedical data mining applications and data analysis workflows.

A service‐oriented environment for data mining, integrating web services as workflow components

Online collaborative genome annotation resource offering a range of tools and information to validate and correct gene annotations.

A Galaxy instance customized for data-intensive computational analyses in microbiology and metagenomics.

OTP = "One Touch Pipeline" is a comprehensive framework for NGS project organization and processing. The application provides support in all steps of this process, including data transfer from temporary to final storage, execution of data quality monitoring programs, alignment of reads to the reference genome and variant calling. It allows full automatization, extended project administration, and full processing control for operators.

Prediction of Amyloid STructure Aggregation is a web server predictor for amyloid aggregation propensity from protein sequences;

To searches user submitted sequences for any combination of Position Weight Matrices (PWMs), primary sequence patterns and structural motifs.

Software to identify defined fragments in biomacromolecules.

Our algorithm for identifying PCA-correlated SNPs takes as input a properly encoded SNP data matrix and outputs a score for each SNP. SNPs corresponding to the highest scores are typically the most informative in reproducing the structure of the population.

Bioinformatics Docker Images Project, a library of over 50 Docker images. 

A platform for interpretation of proteomics identification results from multiple search engines.

Predictor of human deleterious Single Nucleotide Polymorphisms.

A binary classifier for predicting pathogenic variants in coding and non-coding regions.

phylogeny.fr is a web server intended to phylogenetic analyses.It has been designed to let non-specialist as well as expert users execute phylogenetic workflows. These workflows automatically chain programs to  perform different tasks: the identification of homologous sequences, their multiple alignment, the alignment curation, the phylogenetic reconstruction and the graphical representation of the inferred tree.

A phylogenetic inference platform for epidemiological investigations and population studies of bacterial pathogens.

PhyML is a software that estimates maximum likelihood phylogenies from alignments of nucleotide or amino acid sequences. The main strength of PhyML lies in the large number of substitution models coupled to various options to search the space of phylogenetic tree topologies, going from very fast and efficient methods to slower but generally more accurate approaches. PhyML was designed to process moderate to large data sets. In theory, alignments with up to 4,000 sequences 2,000,000 character-long can be processed. PhyML can process data sets made of multiple genes and fit sophisticated substitution models with heterogeneous components across partition elements.

A suite of tools available on the web to predict and analyze protein structure, function and mutations. 

A human protein-protein interaction meta-database employing primary dataset integration via genetic information ontology, which allows the integrated network to be reversibly normalized to any level of genetic reference without loss of source information and enables primary PPI dataset cross-checking. The PICKLE web-based interface allows for the simultaneous query of multiple entities and provides integrated human PPI networks at either the protein or the gene level, at three PPI filtering modes.

Pipeline for Cancer Inference

A pipeline to extract ensemble-level progression models from cross-sectional sequenced cancer genomes.

A dedicated web server for the automatic modeling of immunoglobulin variable domains based on the canonical structure method

An environment for NGS data management and analytics

Web-interface and database providing tools for the management of different plant phenotyping platforms, and the analysis of images and data.

Annotation of plant reference genomes and pangenomes, support and consulting.

An open-source plug-in that provides some of the most popular molecular dynamics (MD) codes with implementations of a variety of different enhanced sampling algorithms and collective variables.

Post-Translational Modifications Mass Spectrometry Calculator (Emerging Service) 

A free web application that simplifies mass spectrometry calculations for post-translationally modified proteins.

An ML-based tool/web-server to (i) predict GPCR-G-protein couplings; (ii) visually inspect the protein sequence and structural features that are responsible for a particular coupling; (iii) suggest mutations to rationally design artificial GPCRs with new coupling properties based on predetermined coupling features