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Databases

  • EPD  •  The Eukaryotic Promoter Database is an annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally. Access to promoter sequences is provided by pointers to positions in nucleotide sequence entries. The annotation part of an entry includes description of the initiation site mapping data, cross-references to other databases, and bibliographic references.  [less]
  • OrthoDB  •  Catalog of eukaryotic orthologous protein-coding genes. OrthoDB explicitly delineates orthologs at each radiation along the species phylogeny. Available protein descriptors, together with Gene Ontology and InterPro attributes, serve to provide general descriptive annotations of the orthologous groups, and facilitate comprehensive database querying. Data sources include proteomes from arthropods, fungi, vertebrates and basal metazoans. [less]
  • SwissRegulon  •  SwissRegulon is a database of genome-wide annotations of regulatory sites. It contains annotations for 17 prokaryotes and 3 eukaryotes. The database frontend offers an intuitive interface showing genomic information in a clear and comprehensible graphical form. [less]
  • smirnaDB  •  smiRNAdb is a database containing expression information for human, mouse, rat, zebrafish, worm and fruitfly small RNAs (mostly miRNAs) [less]
  • OMA  •  OMA is a project that aims to identify orthologs among publicly available, complete genomes. With many hundreds of genomes analyzed to date, OMA is one of the largest projects of its kind. [less]
  • CLIPZ  •  CLIPZ supports the automatic functional annotation of short reads resulting primarily from crosslinking and immunoprecipitation experiments (CLIP) performed with RNA-binding proteins in order to identify the binding sites of these proteins. The functional annotation could be also applied to short reads resulting from other type of experiments such as mRNA-Seq, Digital Gene Expression, small RNA cloning, etc. CLIPZ enables visualization, mining and analysis of data sets.  [less]
  • ElMMo  •  A website to browse miRNA target predictions from the ElMMo algorithm [less]
  • GPSDB  •  GPSDB (Gene and Protein Synonym DataBase) collects gene/protein names, in a species specific way, from several biological resources. A web-based search interface gives access to the database: given a gene/protein name, it retrieves all synonyms for this entity and queries Medline with a set of user-selected terms. [less]
  • ImmunoDB  •  A simple access point to view gene family assignments, annotations and phylogenetic data for insect immune-related genes and gene families. [less]
  • miROrtho  •  miROrtho contains predictions of precursor miRNA genes covering many animal genomes combining evidence from sequence homology and Support Vector Machine classifiers. We provide both consistent extrapolation of already known miRBase families and novel miRNA predictions by our SVM and orthology pipeline. [less]
  • OpenFlu  •  The OpenFlu database (OpenFluDB) is part of a collaborative effort to share observations on the evolution of Influenza virus in both animals and humans. It contains genomic and protein sequences as well as epidemiological data from more than 25'000 isolates. [less]

Tools

  • EPD  •  The Eukaryotic Promoter Database is an annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally. Access to promoter sequences is provided by pointers to positions in nucleotide sequence entries. The annotation part of an entry includes description of the initiation site mapping data, cross-references to other databases, and bibliographic references.  [less]
  • smirnaDB  •  smiRNAdb is a database containing expression information for human, mouse, rat, zebrafish, worm and fruitfly small RNAs (mostly miRNAs) [less]
  • OMA  •  OMA is a project that aims to identify orthologs among publicly available, complete genomes. With many hundreds of genomes analyzed to date, OMA is one of the largest projects of its kind. [less]
  • Association Viewer  •  AssociationViewer is a Java application used to display SNPs in a genetic context. Supplementary data (such as genes or LD plots) is downloaded from various public data sources on the fly and saved locally in a cache. Custom data can be added as supplementary tracks. [less]
  • ChIP-Seq  •  The ChIP-Seq tools are used to analyze ChIP-seq data and other types of mass genome annotation data (MGA).The programs are: a feature correlation tool (ChIP-cor); a tag centering tool (ChIP-center); a signal peak detection tool (ChIP-peak and a partitioning tool (ChIP-part) [less]
  • CLIPZ  •  CLIPZ supports the automatic functional annotation of short reads resulting primarily from crosslinking and immunoprecipitation experiments (CLIP) performed with RNA-binding proteins in order to identify the binding sites of these proteins. The functional annotation could be also applied to short reads resulting from other type of experiments such as mRNA-Seq, Digital Gene Expression, small RNA cloning, etc. CLIPZ enables visualization, mining and analysis of data sets.  [less]
  • COILS  •  COILS is a program that compares a sequence to a database of known parallel two-stranded coiled-coils and derives a similarity score. By comparing this score to the distribution of scores in globular and coiled-coil proteins, the program then calculates the probability that the sequence will adopt a coiled-coil conformation. [less]
  • ElMMo  •  A website to browse miRNA target predictions from the ElMMo algorithm [less]
  • ESTscan  •  ESTScan can detect coding regions (CDS) in DNA sequences, even if they are of low quality. It also detects/corrects sequencing errors that lead to frameshifts. ESTScan is not a gene prediction program , nor is it an open reading frame detector. In fact, its strength lies in the fact that it does not require an open reading frame to detect a coding region. The program may miss a few translated amino acids at termini, but detects coding regions with high selectivity and sensitivity. [less]
  • GMM  •  Gaussian Mixture Model (GMM) detects copy number variation from the distribution of copy number ratios. From the data, it will fit one component for each of the following copy number states: deletion, copy-neutral, 1 and 2 additional copy; with a constraint on the difference between the mixture means. Then for a given individual, it will determine the probabilities for each copy number state and compute the expected copy number (dosage). [less]
  • IScan  •  A package to identify insertion sequences and similar transposable elements, their inverted repeats, and the direct target repeats they generate in entire genomes.  [less]
  • ISMARA  •  MARA models genome-wide expression data in terms of our 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. [less]
  • IsotopIdent  •  Isotopident can estimate the theoretical isotopic distribution of a peptide or protein, a polynucleotide and a chemical compound from its composition (sequence of amino acids expressed in either 1-letter code, sequence of amino acids expressed in 3-letter code, sequence of nucleotides or its chemical formula). Isotopident can also compute its monoisotopic mass. and predict the most likely isotope combination and the exact mass of the given input.  [less]
  • MAMOT  •  C++ program for HMM models [less]
  • Sequence Similarity Maps (SSM)  •  A data mining solution to map thousands of viral isolates (influenza, dengue and FMDV virus). [less]
  • ShoRAH  •  Software to analyse deep-sequencing (NGS) data and reconstruct haplotypes in a genetically heterogeneous sample [less]
  • SSA  •  SSA is a software package for the analysis of nucleic acid sequence motifs that are positionally correlated with a functional site such as a transcription initiation site. The programs provided by this web server are the following: generation of a constraint profile (Cpr); generation of a signal list (SList); generation of a signal occurrence profile (OProf); pattern optimization tool (PatOp); find motifs around functional sites (FindM), and extract sequences around functional sites (FromFPS). [less]
  • TriFLe  •  TRiFLe is a program for simulating TRFs and identifying species by TRF profiling [less]
  • tromer  •  The transcriptome analyser project aims to provide tools to determine and document all the transcribed parts of a genome. The transcribed parts are defined by analysing experimental evidence, like expressed sequence tags (EST) and other mRNA sequences. [less]