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Databases

  • Bgee  •  Bgee is a database to compare expression patterns between animal species. Bgee addresses difficulties such as complex anatomies and diverse sources of data by the use of ontologies and the explicit representation of homology. Homology relationships are defined both between genes and between anatomical features. The main efforts are the annotation of anatomical and developmental terms and their homology relationships, and the annotation and statistical treatment of transcriptome data.  [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]
  • 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]

Tools

  • smirnaDB  •  smiRNAdb is a database containing expression information for human, mouse, rat, zebrafish, worm and fruitfly small RNAs (mostly miRNAs) [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]
  • 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]
  • ExpressionView  •  ExpressionView is an R package that provides an interactive environment to explore biclusters identified in gene expression data. A sophisticated ordering algorithm is used to present the biclusters in a visually appealing layout. From this overview, the user can select individual biclusters and access all the biologically relevant data associated with it. The package is aimed to facilitate the collaboration between bioinformaticians and life scientists who are not familiar with the R language. [less]
  • ISA  •  The Iterative Signature Algorithm (ISA) was designed to reduce the complexity of very large sets of data by decomposing it into so-called "modules". In the context of gene expression data these modules consist of subsets of genes that exhibit a coherent expression profile only over a subset of microarray experiments. Genes and arrays may be attributed to multiple modules and the level of required coherence can be varied resulting in different "resolutions" of the modular mapping. [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]
  • Ping pong algorithm  •  The Ping-Pong Algorithm (PPA) is a method for integrating tabular data sets that share a common dimension. A typical example for this is gene expression across a set of tissues and drug-response data for the same tissues. The PPA finds co-modules in the two data sets, i.e. genes that are co-expressed in some tissues that have similar responses to a subset of the drugs. The co-modules can overlap; the PPA is efficient and scales well to large data sets. A Matlab implementation is provided. [less]
  • SIBsim4  •  SIBsim4 is a modified version of the sim4 program, which is a similarity-based tool for spliced alignments, i.e. for aligning an expressed DNA sequence (EST, mRNA) with a genomic sequence. [less]
  • The Miner Suite  •  A package of bioinformatics tools for data analysis, mainly for microarrays [less]
  • Translate  •  Translation of a nucleotide (DNA/RNA) sequence to a protein sequence. [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]