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Showing 20 records out of 379 total
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Categories: proteomics, genomics - Software type(s): website - tool
SHOPS (SHow OPeron Structures) was developed to analyze the genomic operon context for any group of proteins selected on the basis of a set of sequence or domain identifiers. It uses genome annotations of all available fully sequenced prokaryotes to create a scaled graphical overview of the genomic context around the proteins 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: IT infrastructure - Software type(s): website - tool
SPARQL endpoint providing access to integrated data from various sources (incl. SIB resources) relevant for research on SARS-CoV-2.
keywords: COVID-19
Categories: genomics, (sequence alignment), transcriptomics - Software type(s): CLI - tool
SIBsim4 is a modified version of the sim4 program, which is a similarity-based tool for spliced alignments, i.e. for aligning an expressed DNA sequence (EST, mRNA) with a genomic sequence.
keywords: sequence alignment
Categories: proteomics, (protein modifications) - Software type(s): website, CLI - tool
SignalP predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms: Gram-positive prokaryotes, Gram-negative prokaryotes, and eukaryotes. The method incorporates a prediction of cleavage sites and a signal peptide/non-signal peptide prediction based on a combination of several artificial neural networks.
Categories: proteomics, (similarity search/alignment) - Software type(s): website - tool
SIM finds a user-defined number of best non-intersecting alignments between two protein sequences or within a sequence. Results can be viewed with LALNVIEW, a graphical viewer program for pairwise alignments.
Categories: proteomics, (sequence sites, features and motifs) - Software type(s): website - tool
The Simple Modular Architecture Research Tool allows the identification and annotation of genetically mobile domains and the analysis of domain architectures. Normal SMART, (against UniProtKB and stable Ensembl proteomes), and Genomic SMART, (against complete proteomes) are supported.
keywords: protein domain
Categories: proteomics, (proteomics experiment) - Software type(s): website - tool
LC-MSMS software for small molecule identification, can search both low and high mass precision libraries. Users can search on multiple libraries simultaneously, including privately built ones.
Categories: genomics - Software type(s): website - database/tool
The resource is based on a new 'in silico' approach for identifying regulatory variants. The transcription factor (TF) binding score is computed in both the reference (hg19) and alternate human genome assemblies. The alternate genome assembly is generated by incorporating the alternate allele of common genetic variants (AF>=0.001) from the 1000 Genomes Project. Interesting candidate variants are those SNPs that disrupt, create or change the TF binding score/affinity between the two genomes.
Categories: IT infrastructure - Software type(s): website, CLI - tool
Web services interface to bioinformatics tools
keywords: Taverna
Categories: proteomics, (protein structure) - Software type(s): website - tool
Secondary structure prediction.
Categories: proteomics, (function analysis, protein modifications) - Software type(s): website - tool
Classification and secondary structure srediction of membrane proteins.
Categories: proteomics, IT infrastructure - Software type(s): website - tool
SPARQL playground aims to help newbies to get started with SPARQL. It provides a user friendly interface with a simple dataset and examples.
keywords: network
Categories: genomics, (characterisation/annotation) - Software type(s): website - tool
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. The programs provided by this web server are the following: generation of a constraint profile (Cpr); generation of a signal list (SList); generation of a signal occurrence profile (OProf); pattern optimization tool (PatOp); find motifs around functional sites (FindM), and extract sequences around functional sites (FromFPS).
Categories: systems biology - Software type(s): website - tool
Short Tandem Repeat (STR) analysis is one of the most useful methods in molecular biology which is used to compare specific loci on DNA from two or more samples. A short tandem repeat (STR or microsatellite) is a pattern of two or more nucleotides that are repeated directly adjacent to each other. Search for similarities between your cell line samples and the STR profiles in human cell lines stored in the Cellosaurus knowledgebase for cell lines.
Categories: proteomics, (protein structure) - Software type(s): website - tool
Java-based software for structural alignments of proteins
keywords: sequence alignment
Categories: proteomics, (protein interactions) - Software type(s): website - database
STRING is a database of known and predicted protein-protein interactions. The database contains information from numerous sources, including experimental repositories, computational prediction methods and public text collections. STRING is regularly updated and gives a comprehensive view on protein-protein interactions currently available.
keywords: network
Categories: proteomics - Software type(s): website - database
New COVID-19 oriented version enabling users to explore the host-side of the disease, while keeping a focus on putative COVID-19-interacting human proteins.
keywords: COVID-19, network
Categories: glycomics - Software type(s): website - database
SugarBind covers knowledge of glycan binding of human pathogen lectins and adhesins. Information is collected by experts from articles published in peer-reviewed scientific journals. The data were compiled through an exhaustive search of literature published over the past 30 years by glycobiologists, microbiologists, and medical histologists.
Categories: glycomics - Software type(s): website - tool
SugarSketcher was designed to provide users with a simple and efficient interface for drawing glycan molecules with the logos defined in the Symbol Nomenclature for Glycans (SNFG) . The tool operates in a quick mode in which the top menu shows a limited set of logos or in a normal mode in which the top menu is comprehensive. In either cases, a structure can be drawn from scratch or from a core structure. Structures are exportable as .svg images or in the GlycoCT format.
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