Services: Genes And Genomes

A comprehensive structural variant haplotype map of the Iberian population from high-coverage whole-genome sequencing

Genomicus is a database and a web server that integrates comparative genome data and ancestral genome reconstruction in a fast and intuitive way. It enables users to navigate in genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time. A user-friendly graphical interface allows syntenic comparisons and gene order alignments between pairs of genomes or multiple genomes at different scales: local gene order, karyotypes, matrix plots, etc.  Different phylums such as Vertebrates, Plants, Fungi, Metazoa (as per Ensembl Genomes) are represented and regularly updated, as well as specific versions on Tunicates, Fish and Amphioxus.  

A versatile software package for pan-genome analysis, including GET_HOMOLOGUES and GET_HOMOLOGUES-EST

GnpIS is an interoperable Information System for plant and pest genomics. It is a powerful multispecies centralized information system with seven linked relational databases. 

The UniProt  GO annotation program (GOA) aims to provide high-quality Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB).

The NHGRI-EBI GWAS Catalog is a quality-controlled, manually curated, literature-derived collection of all published genome-wide association studies.
 

Performs haplotype assembly from long gapless reads.

Enables you to set up and train models for ab initio prediction of gene structure. That is, to perform "gene calling" and identify which base pairs in a genome belong to the UTR/CDS/Intron of genes.

Human Endogenous RetroViruses Database.

HUGO Gene Nomenclature Committee, responsible for approving unique symbols and names for human loci, including protein coding genes, ncRNA genes and pseudogenes, to allow unambiguous scientific communication.

A web tool for the interpretation of the consequences of the combined changes of gene expression levels and/or genomic mutations in the context of signalling pathways. 

Database of human mitochondrial genomes from primary INSDC databases, personal submissions and application of MtoolBox to NGS data.

A collection of web resources for working with proteins, drug reactions, gene expression analysis, proteome profiling and assessing MinION Data, including: 

• DeSeq2 - an R/Bioconductor package for differential expression analysis of high-throughput sequencing assays
• DexSeq - an extension of DESeq for the analysis of alternative exon usage.
• EBImage - R/Bioconductor package that provides general purpose functionality for the reading, writing, processing and analysis of images.
• SMART - a web resource providing simple identification and extensive annotation of protein domains via sequence homology searches.
• SIDER - a web-based resource that contains information on marketed medicines and their recorded adverse drug reactions.

A population-based database that collects all the cases with malignancies in Hungary by reports of oncology care hospitals. Registration is mandatory. The Registry is regulated by the order of the Hungarian Government and maintained by the  National Institute of Oncology.

An integrated knowledge resource specialized in the immunoglobulins (IG) or antibodies, T cell receptors (TR), and major histocompatibility (MH) of human and other vertebrate species. 

Non-coding genome sequences and genetic network tools. The IRESite presents experimental evidence of many eukaryotic viral and cellular internal ribosome entry site (IRES) regions.

Models genome-wide expression data in terms of genome-wide annotations of regulatory sites. For a given expression data-set it infers the key transcription regulators, their sample- dependent activities, and their genome-wide targets. 

Interactive Tree Of Life (iTOL) is an online tool for the display and manipulation of phylogenetic trees. It provides a large variety of tree layouts, drawing and annotation features including circular tree layout, which is well-suited particularly for mid-sized trees (up to several thousand leaves). Tree displays can be exported in several graphical formats, both bitmap and vector based. Part of the Microbiome Analysis Toolbox. 

ITSoneDB is a comprehensive collection of eukaryotic ribosomal RNA Internal Transcribed Spacer 1 (ITS1) sequences.

Jalview is a Win/Mac/Linux/Web interactive graphical interface and command line tool for molecular sequence, alignment and 3D structure bioinformatics resource interoperability.

A comprehensive approach for supporting evidence-based gene discovery and complex trait analysis across species. KnetMiner is a web application to search and visualise genome-scale knowledge networks. It is used by scientists in academia and industry to accelerate gene-trait discovery research. KnetMiner offers features such as keyword, gene list and genome region search, query refinement, gene ranking, gene set enrichment analysis and interactive visualisation of knowledge networks and genomic information.

Species focused genome data resource for sea lice, provides a genome browser, access to high-throughput data and LIMS.

LoRDEC is a standalone software for error correcting long reads (from Pacific Biosciences, or Oxford Nanopore) with a hybrid approach. LoRDEC uses short reads to correct long reads; it combines sequencing data from both the second and third generation technologies. It can be easily integrated in any pipeline for processing deep sequencing data. LoRDEC's originality is to build a graph that summarize all short reads, and then to align the long reads against this graph to correct them. This makes LoRDEC a very efficient tool to process large datasets. It has been widely used in whole genome or transcriptome projects around the world.

dSysMap (Mapping of Human disease-related mutations at the systemic level) displays Human disease-related mutations on the structural interactome. Mapping of mutations on protein structures and on interaction interfaces allows you to visualize the region of the interactome that they affect and helps in rationalizing their mechanism of action.

Freely accessible microbial genomics and metagenomics reference databases that include MarRef, MarDB, and MarCat. The MMP also includes a search engine that you can use to query all three databases at once.

Development of the software plattform for MassBank, a database of reference spectra from different instruments, including high-resolution mass spectra of small metabolites (<3000 Da).

Parallel and scalable workflow for the analysis of Oxford Nanopore direct RNA sequencing datasets. Nextflow pipeline for analysis of Nanopore reads (from RNA/cDNA/DNA).

A tool for genome scaffolding that exploits information obtained from a set of (draft or closed) genomes to determine the correct order and orientation of the contigs.

MEM is a web-based multi experiment gene expression query and visualization tool. It gathers thousands of publicly available gene expression data sets from ArrayExpress database.

Interactive viewer of metadynamics results.