Bioinformatic services
Bioconductor
Huber Group, A bridge from R to BioMart databases - for instance Ensembl
Huber Group, Analysis of cell-based high-throughput screens
Huber Group, Image processing and analysis toolkit for R
Huber Group, Visualize long vectors of data by means of Hilbert curves
Huber Group, Analysis of ChIP-chip data
Huber Group, Transcript mapping with high-density oligonucleotide tiling arrays
Huber Group, Normalization and variance stabilizing transformation of microarray data.
Database
EBI External Services, The EMBL Nucleotide Sequence Database constitutes Europe's primary nucleotide sequence resource.
EBI ENSEMBL, Ensembl annotates known genes and predicts new ones, with functional annotation from InterPro, OMIM, SAGE and gene families.
Gene Analysis
Bork Group, Gene analysis in genomic regions
Gene Expression
Arendt Group, A database for cross species gene expression data acquired through high-resolution in situ experiments
Arendt Group, A database for medaka gene expression data acquired through high-resolution in situ experiments.
Homology and Similarity
Gibson Team, Flexible retrieval of homologous protein sequences.
Gibson Team, Please note that the server is currently down. It will be made available as soon as possible.
Gene2EST is a BLAST2 server for searching EST databases with eukaryotic gene sequences. The query can be big [>=100 KB] to span large highly spliced genes. As well as the BLAST output, the user can retrieve [1] an alignment of the ESTs matching the gene and [2] output for graphical display with Artemis that can show alternative splicing.
Gene2EST is a BLAST2 server for searching EST databases with eukaryotic gene sequences. The query can be big [>=100 KB] to span large highly spliced genes. As well as the BLAST output, the user can retrieve [1] an alignment of the ESTs matching the gene and [2] output for graphical display with Artemis that can show alternative splicing.
Bork Group, Mass Spectrometry driven BLAST
Bork Group, Identification of protein repeats and statistical significance of sequence comparisons
Gibson Team, SIR provides the ability to simultaneously search a protein database with a sequence motif pattern and keywords, e.g. useful for restricting a pattern search to a database subset.
Bork Group, Advanced WU-BLAST Search with post-processing
Phylogeny
Bork Group, Evolutionary genealogy of genes: Non-supervised Orthologous Groups
Bork Group, Interactive Tree Of Life - an online tool for the display and manipulation of phylogenetic trees
Bork Group, Phylogenetic analysis of metagenomics sequence data
Protein Function Analysis
Structural and Computational Biology Unit, ADAN database offers the FOLD-X scoring matrices for ligand predictions and putative partners from protein domains when available, as well as homology models. A querying function allows the user to input a polypeptide sequence and retrieve the putative binding segments for a particular domain.
Pepperkok Team, The Bioinformatic Harvester collects and displays bioinformatic protein information and predictions for human proteins from various databases for realtime access. The Marvester does the same for mouse proteins.
Bork Group, Candidate Genes to Inherited Diseases
Pepperkok Team, Localisation and functional characterisation of gfp-tagged novel human cDNAs
Bork Group, Manually Annotated Targets and Drugs Online Resource
Bork Group, General graph visualisation tool
Gibson Team, Phospho.ELM provides a linked database of experimentally verified phosphorylation sites in eukaryotic proteins.
Russell Group (Visiting), Prediction Of Unknown protein functional Sub-Types
Bork Group, Simple Modular Architecture Research Tool
Structural and Computational Biology Unit, NPeffect analyses the effect of coding, non-synonymous SNPs on 3
categories of functional and physico-chemical properties of the affected
proteins, namely protein structure and dynamics [stability, aggregation,
dynamics,..], integrity of functional sites and cellular processing.
categories of functional and physico-chemical properties of the affected
proteins, namely protein structure and dynamics [stability, aggregation,
dynamics,..], integrity of functional sites and cellular processing.
Bork Group, A resource to explore known and predicted interactions of chemicals and proteins
Bork Group, Search Tool for the Retrieval of Interacting Genes/Proteins
Gibson Team, Investigation of functional sites in protein sequences with the Eukaryotic Linear Motif database.
Sequence Analysis
Korbel Group, Nucleotide-resolution genotyping of structural variants in personal genomics data
Bork Group, Shared Ortholog and Gene Order Tree Reconstruction Tool
Structural Analysis
Meyer-Klaucke Team, Automated analysis of EXAFS data.
Structural and Computational Biology Unit, An algorithm to predict the helical content of peptides
Bork Group, Annotation of Domains
Lamzin Group, Automated model building of protein structures, version 7.0.1.
Svergun Group, A programme suite for small-angle scattering data analysis of biological macromolecules.
Svergun Group, A Web interface to major programmes from the ATSAS 2.2 suite for small-angle scattering data analysis from biological macromolecules.
Tucker Group, A platform for automated crystal structure determination. Starting from scaled diffraction data, an interpretable electron density map or a partial model are typically achieved within minutes of submission of the job.
Lamzin Group, Advanced Diffraction Data Collection Strategy programme.
Gibson Team, DisEMBL is a disorder predictor targetted at Structural Genomics Initiatives.
Structural and Computational Biology Unit, Force field for energy calculations in proteins
Gibson Team, GlobPlot is a server for exploring disorder or globularity in protein sequences.
Russell Group (Visiting), Interaction Prediction through Tertary Structure
Russell Group (Visiting), Patterns In Non-homologous Tertiary Structure: Comparison/Search of structural patterns (in 3D)
Bork Group, Prediction of functional effect of human nsSNPs
Schneider (Thomas) Group, Structure superposition and identification of rigid domains
Structural and Computational Biology Unit, Software for predicting protein aggregation
Lamzin Group, Automated crystal identification and centring on a beamline goniostat, version 3.0.
Systems Biology Software
Structural and Computational Biology Unit, A cell network simulation program supporting localisation and diffusion by using a mesoscopic stochastic reaction model.
Text Mining
Schneider (Reinhard) Team, Biomedical knowledge management system based on Medline abstracts
Bork Group, Literature Support for Alternative Transcripts
Schneider (Reinhard) Team, Automated annotation of biochemical terms in PDF, Text and Microsoft Office documents
Schneider (Reinhard) Team, Automated annotation of biochemical terms in web pages
Bork Group, Explore a bibliographic search in MEDLINE
Visualization
Schneider (Reinhard) Team, Visualization of biological networks in 3D
Huber Group, Visualization of genomic data with the Hilbert curve
Schneider (Reinhard) Team, System for displaying 3D structures integrated with sequences and features
Miscellaneous
Korbel Group, Inference of genomic structural variants (deletions, insertions, and inversions) from next-generation DNA sequencing data.
Schneider (Reinhard) Team, The Sequence Retrieval System is a search tool to do a fast full text search in different databases including the EMBL DNA database.