The Computational Cancer Genomics (CCG) group of the Swiss Institute of Bioinformatics (SIB) is dedicated to the development of analysis tools and databases relating molecular sequences and biological functions.

[EPD] [ChIP-Seq] [SSA] [TagScan] [ZFN-Site] [UCNEbase] [TROMER] [MADAP] [PWMTools] [HTPSELEX] [CleanEx] [Documentation] [Links]

Databases and Tools
  • EPD - The Eukaryotic Promoter Database.
    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. It provides information about eukaryotic promoters available in the EMBL Data Library and is intended to assist experimental researchers, as well as computer analysts, in the investigation of eukaryotic transcription signals.

  • TagScan - An online tool for finding short exact matches in large sequence databases
    TagScan allows searching for perfect matches and for single or double nucleotide mismatches between oligonucleotide queries of up to 60 bases and sequence databases comprising entire genomes or mRNA reference sequences. The smallest query allowed is 10 nucleotides long.
    TagScan is the Web portal to the Tagger project, whose aim is to provide tools for finding short exact matches in large sequence databases.

  • ZFN-Site - Genome-wide tag scanner for nuclease off-sites
    Based on the TagScan tool, this application is intended to search genomes for specific target sites and off-target sites, such as for pairs of zinc finger proteins (ZFPs), zinc finger nucleases (ZFNs) and modified homing endonucleases. This can either define a zinc finger nucleases (hetero-dimer) or allow for homo-dimers depending on the status of the checkbox in the input form.

  • UCNEbase - A database for ultraconserved noncoding elements and genomic regulatory blocks
    UCNEbase provides information on the evolution and genomic organization of ultra-conserved non-coding elements (UCNEs) in multiple vertebrate species. It currently covers 4351 such elements in 18 different species. Around half of these elements are located within intergenic regions (2139) and the rest are located within non-coding parts of genes: introns (1713) and UTRs (499). The majority of UCNEs are supposed to be transcriptional regulators of key developmental genes.
  • ChIP-Seq - The ChIP-Seq Analysis server
    The ChIP-Seq Web Server provides access to a set of useful tools performing common ChIP-Seq data analysis tasks, including positional correlation analysis, peak detection, and genome partitioning into signal-rich and signal-poor regions. Users can analyse their own data by uploading mapped sequence tags in various formats, including BED and BAM. The server also provides access to hundreds of publicly available data sets such as ChIP-seq data, RNA-seq data (i.e. CAGE), DNA-methylation data, sequence annotations (promoters, polyA-sites, etc.), and sequence-derived features (CpG, phastCons scores).

  • SSA - The Signal Search Analysis server
    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 for instance. The possible analysis includes Occurence Profile plots, generation of a signal list, generation of a constraint profile, pattern optimization as well as finding motifs around functional sites.

  • PWMTools - Position Weght Matrix model generation and evaluation tools
    PWMTools is a Web interface for Position Weight Matrix (PWM) model generation and evaluation. It includes the following tools: MSeq which is a software pipeline used to derive TFBS models from DNA sequences such as HT-SELEX and MITOMI-seq, PWMEval and PWMScore that are tools used to evaluate PWM models based on ChIP-seq data, and PWMScan which is a tool to scan entire genomes of common model organisms with a PWM.
  • HTPSELEX - A database of in vitro selected TFBS sequences obtained with high-throughput SELEX
    The HTPSELEX database contains sets of in vitro selected transcription factor binding site sequences obtained with the high-throughput SELEX (HTPSELEX) method. In addition the database also contains binding sites obtained with conventional SELEX method.

Databases and Tools maintained in collaboration with other SIB groups
  • TROMER - The transcriptome analyser (TROMER) project
    The transcriptome analyser (TROMER) project aims to provide tools to determine and document all the transcribed elements of a genome. The transcriptome data include transcribed regions, splice variants, SAGE mappings, MPSS mappings, Affymetrix chips mappings, etc., for several organisms.

  • MADAP - A clustering tool for one-dimensional genome annotation data mapped onto genome sequences.
    MADAP identifies groups of data corresponding to one or several genomic sites, and estimates the volume and extension of such groups (clusters). Input data might be obtained from cDNA and tag sequencing protocols to map the 5' and 3'ends of mRNA, from ChIP-chip analysis, or from genome-wide SNP-typing.

Databases and Tools maintained by former collaborators
  • CleanEx - The gene expression database and cross-dataset analysis tool
    CleanEx provides access to public gene expression data via unique approved gene symbols. It represents heterogeneous expression data produced by different technologies in a way that facilitates joint analysis and cross-dataset comparisons.

Documentation Links to other Resources
  • ENSEMBL - ENSEMBL Genome Browser
  • UCSC - UCSC Genome Browser

  • Entrez - NCBI Entrez cross-database search page
  • MyHits - A database and web tools devoted to protein domains

  • SIB course portal - SIB Bioinformatics course portal

Last update 27 Sep. 2012