Bioinformatic services
Bioconductor
| biomaRt | Huber Group, A bridge from R to BioMart databases - for instance Ensembl |
| cellHTS2 | Huber Group, Analysis of cell-based high-throughput screens |
| DESeq | Huber Group, Testing for differential expression in RNA-Seq and other count data |
| EBImage | Huber Group, Image processing and analysis toolkit for R |
| genomeIntervals | Huber Group, Operations on genomic intervals such as merging, overlap detection, or computing distances between intervals |
| HilbertVis | Huber Group, Visualize long vectors of data by means of Hilbert curves |
| mgsa | Steinmetz Group, Model-based Gene Set Analysis(MGSA), a Bayesian modelling approach for gene set enrichment |
| Ringo | Huber Group, Analysis of ChIP-chip data |
| tilingArray | Huber Group, Transcript mapping with high-density oligonucleotide tiling arrays |
| vsn | Huber Group, Normalization and variance stabilizing transformation of microarray data. |
Database
| EMBL Nucleotide Sequence Database | EBI External Services, The EMBL Nucleotide Sequence Database constitutes Europe's primary nucleotide sequence resource. |
| Ensembl | EBI ENSEMBL, Ensembl annotates known genes and predicts new ones, with functional annotation from InterPro, OMIM, SAGE and gene families. |
High-throughput sequencing
| CopySeq | Korbel Group, Discovery and copy-number genotyping of genomic structural variants |
| HTSeq | Huber Group, A Python package for processing and analysing data from high-throughput sequencing assays |
| PEMer | Korbel Group, Discovery of genomic structural variants by high-throughput and massive paired-end mapping |
Gene Expression
| 4DXpress | Arendt Group, A database for cross species gene expression data acquired through high-resolution in situ experiments |
| MEPD | Arendt Group, A database for medaka gene expression data acquired through high-resolution in situ experiments. |
| PEPD | Arendt Group, |
Homology and Similarity
| MSBLAST | Bork Group, Mass Spectrometry driven BLAST |
| REPeats in proteins | Bork Group, Identification of protein repeats and statistical significance of sequence comparisons |
| WU-BLAST2 | Bork Group, Advanced WU-BLAST Search with post-processing |
Microscopy
| Micropilot | Pepperkok Team, Micropilot is a microscopy software that can be rapidly trained to automatically identify cells of interest. |
Phylogeny
| eggNOG |
Bork Group, Evolutionary genealogy of genes: Non-supervised Orthologous Groups |
| iTOL | Bork Group, Interactive Tree Of Life - an online tool for the display and manipulation of phylogenetic trees |
| MLTreeMap | Bork Group, Phylogenetic analysis of metagenomics sequence data |
Protein Function Analysis
| ADAN | 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. |
| Bioinformatic Harvester | 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. |
| EpiC |
Gibson Team, EpiC applies protein structure-function information to help identify target epitopes for antibody design |
| Genes2Diseases | Bork Group, Candidate Genes to Inherited Diseases |
| gfp-cDNA | Pepperkok Team, Localisation and functional characterisation of gfp-tagged novel human cDNAs |
| MATADOR | Bork Group, Manually Annotated Targets and Drugs Online Resource |
| Medusa | Bork Group, General graph visualisation tool |
| Phospho.ELM | Gibson Team, Phospho.ELM provides a linked database of experimentally verified phosphorylation sites in eukaryotic proteins. |
| SMART | Bork Group, Simple Modular Architecture Research Tool |
| SNPeffect | 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. |
| STITCH | Bork Group, A resource to explore known and predicted interactions of chemicals and proteins |
| STRING | Bork Group, Search Tool for the Retrieval of Interacting Genes/Proteins |
| The ELM Server | Gibson Team, Investigation of functional sites in protein sequences with the Eukaryotic Linear Motif database. |
Sequence Analysis
| Alignment tools | Bork Group, |
| BLAST SK1/ YJM789/S288c | Steinmetz Group, BLAST server for assembled genomes from S. cerevisiae strains SK1, YJM789, and S288c |
| BreakSeq | Korbel Group, Nucleotide-resolution genotyping of structural variants in personal genomics data |
| SHOT | Bork Group, Shared Ortholog and Gene Order Tree Reconstruction Tool |
| Trawler | Arendt Group, |
Structural Analysis
| AGADIR | Structural and Computational Biology Unit, An algorithm to predict the helical content of peptides |
| AnDom | Bork Group, Annotation of Domains |
| ARP/wARP | Lamzin Group, Automated model building of protein structures, version 7.1 |
| ATSAS |
Svergun Group, A programme suite for small-angle scattering data analysis of biological macromolecules. |
| ATSAS-ONLINE | Svergun Group, A Web interface to major programmes from the ATSAS 2.2 suite for small-angle scattering data analysis from biological macromolecules. |
| Auto-Rickshaw | Lamzin Group, The EMBL Hamburg automated crystal structure determination platform |
| BEST | Lamzin Group, Advanced Diffraction Data Collection Strategy programme. |
| DisEMBL | Gibson Team, DisEMBL is a disorder predictor targetted at Structural Genomics Initiatives. |
| FOLDX: Tools for Protein Design | Structural and Computational Biology Unit, Force field for energy calculations in proteins |
| GlobPlot | Gibson Team, GlobPlot is a server for exploring disorder or globularity in protein sequences. |
| PolyPhen | Bork Group, Prediction of functional effect of human nsSNPs |
| Rapido | Schneider (Thomas) Group, Structure superposition and identification of rigid domains |
| TANGO | Structural and Computational Biology Unit, Software for predicting protein aggregation |
| XREC | Lamzin Group, Automated crystal identification and centring on a beamline goniostat, version 3.1 |
Systems Biology Software
| SmartCell | Structural and Computational Biology Unit, A cell network simulation program supporting localisation and diffusion by using a mesoscopic stochastic reaction model. |
Text Mining
| AKS (almaKnowledge Server) | Schneider (Reinhard) Team, Biomedical knowledge management system based on Medline abstracts |
| LSAT | Bork Group, Literature Support for Alternative Transcripts |
| OnTheFly | Schneider (Reinhard) Team, Automated annotation of biochemical terms in PDF, Text and Microsoft Office documents |
| Reflect | Schneider (Reinhard) Team, Automated annotation of biochemical terms in web pages |
| XplorMed | Bork Group, Explore a bibliographic search in MEDLINE |
Visualization
| Arena3D | Schneider (Reinhard) Team, Visualization of biological networks in 3D |
| HilbertVis | Huber Group, Visualization of genomic data with the Hilbert curve |
| SRS3D | Schneider (Reinhard) Team, System for displaying 3D structures integrated with sequences and features |
Miscellaneous
| BreakPtr |
Korbel Group, Mapping copy-number variation with high-density oligonucleotide tiling arrays. |
| PEMer | Korbel Group, Discovery of genomic structural variants by high-throughput and massive paired-end mapping |
| Sequence Retrieval System SRS | 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. |