| Databases
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Tools
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EPD - The Eukaryotic Promoter Database.
The Eukaryotic Promoter Database is an annotated non-redundant collection of eukaryotic POL II promoters. 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.
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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.
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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. Each entry in the database corresponds to one HTP SELEX or conventional SELEX experiment.
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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.
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ChIP-Seq - The ChIP-Seq Analysis server
The ChIP-Seq tools are used to analyze data produced by chIP-seq experiments and other type of mass genome annotation data (MGA).
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| Databases maintained in collaboration with other SIB groups
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Tools maintained in collaboration with other SIB groups
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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.
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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.
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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.
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| Documentation
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Links to other Resources
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Publications - List of publications of the CCG group members
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Linking CCG - How to create HTML links to CCG databases
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Genomes table - Current Genome assemblies stored at SIB
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EMBnet - The EMBnet Swiss Node
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MyHits - A database and web tools devoted to protein domains
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ENSEMBL - ENSEMBL Genome Browser
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UCSC - UCSC Genome Browser
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Entrez - NCBI Entrez cross-database search page
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