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Showing 5 records out of 5 total

Categories: genomics, (characterisation/annotation) - Software type(s): website, CLI - 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)
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.
Categories: proteomics, genomics, systems biology - Software type(s): website, databases files - database/tool
This is both a tool and a database. Via a web service, users can generate i) integrated proteogenomics databases (iPtgxDBs) that can be used to identify as of yet missing protein-coding genes in prokaryotic organisms, and ii) a GFF file that contains all integrated annotations from reference genome annotations, gene prediction softwares like Prodigal, and a modified 6-frame translation (considering alternative start codons). Users are encouraged to make their iPtgxDBs available.
Categories: proteomics, (protein modifications), genomics, (characterisation/annotation), systems biology, transcriptomics - Software type(s): website, GUI - 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.
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.