Service list

A Consensus Method for Amyloid Propensity Prediction

ANASTASIA (Automated Nucleotide Animoacid Sequences Translational plAtform for Synthetic Interpretation and Analysis) is a metagenomics analysis platform and repository.

http://motherbox.chemeng.ntua.gr/anastasia_dev/

ANISEED is the main model organism database for the worldwide community of scientists working on a class of marine invertebrates, the tunicates (sister-group of vertebrates). It integrates for each species: a main knowledge base with extended information on gene function, gene expression, phylogeny and embryonic anatomy at single cell resolution; a genomic browser and a Genomicus gene synteny browser.

Annotates variants with biological data such as protein structural information, functionally important residues, conservation of functional domains and evidence of cross-species conservation.

Annotation Retrieval of Gene Ontology Terms using semantic similarity in Gene Ontology.

Automated high-throughput assembly, annotation and feature analysis of microbial genome cohorts

BacDive represents a collection of organism-linked information covering the multifarious aspects of bacterial and archaeal biodiversity. The content encloses information on taxonomy, morphology, physiology, sampling and environmental conditions as well as molecular biology.

Bakta is a tool for the rapid and standardised annotation of bacterial genomes and plasmids. It provides dbxref-rich and sORF-including annotations in machine-readable JSON and bioinformatics standard file formats for automatic downstream analysis.

Online access to tools and databases related to miRNAs binding site predictions, RNA Binding protein binding sites, circular RNAs, CLIP data analysis and transcriptome analysis

Database to retrieve and compare gene expression patterns between animal species. 

BioSamples stores and supplies descriptions and metadata about biological samples used in research and development by academia and industry. 

Primer design and ePCR method for bisulfite treated and untreated DNA sequences (cDNA, genomic)

General‐purpose software for making genotype–phenotype data discoverable in restricted or open access contexts.

An online platform for testing the enrichment of cancer hallmark genes

Functional platform for gene expression changes and mutational status in solid tumours

An R package that incorporates most state-of-the-art deconvolution methods, into an intuitive and extendible framework, providing a single entry point to explore, assess and disentangle gene expression data from heterogeneous samples.

A comprehensive resource of channels, pores and tunnels found in biomacromolecular structures deposited in the Protein Data Bank.

ChIPSummitDB is a comprehensive database of transcription factor binding sites verified by human ChIP-seq experiments

ClustVis is a web tool for visualizing clustering of multivariate data. This web tool allows users to upload their own data and easily create Principal Component Analysis (PCA) plots and heatmaps.

Collaborative Spanish Variant Server (CSVS) is a crowdsourcing initiative to provide information about the genomic variability of the Spanish population to the scientific/medical community.

Supports Finnish national data custodians (biobanks) in building a data resource for Sequence Initiative Suomi and affiliated projects.

Web based portal of organism-specific cross-platform expression compendia of bacterial organisms and grapevine

Aligns contigs from a draft genome to a closely related genome, and resolves their relative orientation based on this alignment.

COPO is a portal for scientists to describe, store and retrieve data more easily, using community standards and public repositories that enable the open sharing of results. COPO can link your outputs to your ORCiD profile.

Galaxy server allowing to align complete assemblies of SARS-CoV-2 genomes with the reference genomic sequence to obtain a list of polymorphic positions and to annotate genetic variants.

A data resource for Quercus suber.

Template-based predictor of RNA secondary structure. It takes a template RNA secondary structure(s) and a query RNA sequence(s) and generates secondary structure of the query sequence(s) using the provided structure(s) as a template(s). Biological reliability of the generated structures is evaluated in form of z-scores.

CRISPRCas++ is a new website holding a program called CRISPRCasFinder to detect CRISPR arrays and cas genes in the genome of prokaryotes. CRISPRCasMeta is adapted to the analysis of large metagenomic data. The programs are available online or can be downloaded for local usage. A database called CRISPRCasdb, the successor of CRISPRdb, is accessible on the CRISPRCas++ website. It can be browsed and queried in search for repeat and spacer sequences. 

Chipster is a user-friendly analysis software for high-throughput data. It contains hundreds of analysis tools for next generation sequencing (NGS), microarray, proteomics and sequence data. 

Curare is a free analysis pipeline for reproducible, high-throughput, bacterial RNA-Seq experiments. Define standardized pipelines customised for your specific workflow, without installing all the tools by yourself.