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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)
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.
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: Affymetrix chip analysis, animal, arthropod, Bayesian network, ChIP-seq, eukaryotic promoter, expression, expression data, fungi, genetic data analysis, genomics, graphics, HMM, human, insect, in situ hybridization, interaction, maximum likelihood, microarray, network, NGS, regulatory site, sequence analysis, sequencing, transcription factor binding site, transcription module, transcription regulation, transcription start site annotation, transcriptome analysis, vertebrate
Swissregulon is a database of genome-wide annotations of regulatory sites. Swissregulon contains annotations for 17 prokaryotes and 3 eukaryotes. The database frontend offer easy and intuitive interface showing genomic information in clear and comprehensible graphical form.
keywords: alignment, animal, arthropod, bacteria, binding sites prediction, ChIP-seq, database searching, eukaryotic promoter, fungi, genetic data analysis, genomics, graphics, human, insect, in situ hybridization, interaction, kinase regulator interaction, multiple sequence alignment (MSA), network, NGS, population genetics, protein interaction, regulatory site, selection, sequence analysis, sequence comparison, sequence retrieval, short sequence alignment, transcription factor binding site, transcription module, transcription regulation, transcription start site annotation, transcriptome analysis, two component system, vertebrate