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Showing 4 records out of 4 total

ChIP-Seq [SIB: Computational Cancer Genomics group]
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Categories: genomics, (characterisation/annotation) - Software type(s): CLI, website - tool
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)
keywords: ChIP-seq, next generation sequencing (NGS), promoter, transcription factor binding site, transcription regulation, transcription start site annotation
EPD [SIB: Computational Cancer Genomics group]
[download] UP
Categories: genomics, (characterisation/annotation) - Software type(s): website - database/tool
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.
keywords: promoter, transcription regulation, transcription start site annotation
ISMARA [SIB: Genome Systems Biology group]
UP
Categories: proteomics, (post-translational modification), genomics, (characterisation/annotation), systems biology, transcriptomics - Software type(s): GUI, website - tool
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.
keywords: Bayesian network, ChIP-seq, hidden markov model (HMM), maximum likelihood, network, next generation sequencing (NGS), promoter, sequence analysis, transcription factor binding site, transcription module, transcription regulation, transcription start site annotation
SwissRegulon [SIB: Genome Systems Biology group]
UP
Categories: genomics, (characterisation/annotation), systems biology, transcriptomics - Software type(s): website - database
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.
keywords: ChIP-seq, network, next generation sequencing (NGS), promoter, sequence alignment, sequence analysis, short sequence alignment, transcription factor binding site, transcription module, transcription regulation, transcription start site annotation