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Showing 8 records out of 8 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: proteomics, (sequence sites, features and motifs), systems biology - Software type(s): website - tool
CRUNCH - A completely automated pipe-line for ChIP-seq data analysis, starting from raw sequencing reads, through quality filtering, read mapping, fragment size estimation, peak calling, peak annotation and comprehensive regulatory motif analysis. It runs with data from human (hg19), mouse (mm9) or drosophila (dm3).
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, (sequence alignment, similarity search), systems biology - Software type(s): website, CLI, GUI - tool
Phylogibbs is an algorithm for discovering regulatory sites in a collection of DNA sequences, including multiple alignments of orthologous sequences from related organisms.The algorithm uses a Gibbs sampling strategy, takes the phylogenetic relationships of the input sequences rigorously into account, and assigns realistic posterior probabilities to reported sites using a novel annealing+tracking strategy.
Categories: genomics, transcriptomics - Software type(s): library - tool
QuasR: R/Bioconductor package for the quantification and analysis of Short Reads. It covers a complete workflow starting from raw sequence reads, over creation of alignments and quality control plots, to the quantification of genomic regions of interest.
Categories: genomics, (characterisation/annotation) - Software type(s): CLI - tool
Software to analyse deep-sequencing (NGS) data and reconstruct haplotypes in a genetically heterogeneous sample
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.