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Showing 20 records out of 369 total
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Categories: proteomics, (function analysis), systems biology - Software type(s): website - database
Rhea is a comprehensive and non-redundant resource of expert curated biochemical reactions described using species from ChEBI (Chemical Entities of Biological Interest). Rhea has been designed for the functional annotation of enzymes and the description, analysis and reconciliation of genome-scale metabolic networks. Rhea reactions are extensively curated with links to source literature and are mapped to other resources such as SwissLipids, MetaNetX, Reactome, BioCyc and KEGG.
Categories: proteomics, (protein structure) - Software type(s): website - tool
This server finds similar protein sequences in NR and aligns them, providing sequence logos that show relative conservation of different positions. Local structure predictions are done with neural nets for several different local structure alphabets, and hidden Markov models are created. Fold recognition and alignment to proteins in the Protein Data Bank are done, and a full three-dimensional model is constructed.
Categories: similarity search/alignment, similarity search - Software type(s): website - tool
SAMBA is a 128 processor array for speeding up the comparison of biological sequences. The hardware implements a parameterized version of the Smith and Waterman algorithm allowing the computation of local or global alignments with or without gap penalty.
keywords: sequence alignment
Categories: proteomics, (function analysis) - Software type(s): website - tool
SAPS (Statistical Analysis of Protein Sequences) evaluates a wide variety of protein sequence properties using statistics. Properties considered include compositional biases, clusters and runs of charge and other amino acid types, different kinds and extents of repetitive structures, locally periodic motifs, and anomalous spacings between identical residue types.
Categories: proteomics, (sequence sites, features and motifs) - Software type(s): website, CLI - tool
Scan protein sequence(s) against PROSITE, or search for hits by specific motif(s) in protein sequence database(s). ScanProsite may be used alternatively in quick scan mode or advanced scan mode.
Categories: proteomics, (protein structure) - Software type(s): website - tool
SCRATCH is a server for predicting protein tertiary structure and structural features. The SCRATCH software suite includes predictors for secondary structure, relative solvent accessibility, disordered regions, domains, disulfide bridges, single mutation stability, residue contacts versus average, individual residue contacts and tertiary structure.
Categories: proteomics, (protein modifications) - Software type(s): website - tool
The SecretomeP 2.0 server produces ab initio predictions of non-classical i.e. not signal peptide triggered protein secretion. The method queries a large number of other feature prediction servers to obtain information on various post-translational and localizational aspects of the protein, which are integrated into the final secretion prediction.
Categories: evolutionary biology - Software type(s): website - database
Selectome is a database of positive selection based on a rigorous branch-site specific likelihood test. Positive selection is detected using CODEML on all branches of animal gene trees. The web interface of Selectome enables queries according both to the results of positive selection tests, and to gene related criteria. Test results including positively selected sites can be visualized on the tree, and on the protein sequence alignment.
Categories: proteomics, (sequence sites, features and motifs, similarity search/alignment) - Software type(s): website - tool
Seq2Logo is a web-based sequence logo method for construction and visualization of amino acid binding motifs and sequence profiles including sequence weighting, pseudo counts and two-sided representation of amino acid enrichment and depletion.
Categories: proteomics, (sequence sites, features and motifs, similarity search/alignment) - Software type(s): website - tool
SeqLogos generates sequences logos from amino acid sequence alignment. Sequences logos are useful tools to visualize sequence patterns and represent a more informative alternative to consensus sequence
Categories: proteomics, genomics, (characterisation/annotation) - Software type(s): website - tool
A data mining solution to map thousands of viral isolates (influenza, dengue and FMDV virus).
keywords:
Categories: similarity search/alignment - Software type(s): website - tool
This server calculates the variability in each column of a multiple sequence alignment using the Shannon entropy (H) function.
keywords: alignment analysis
Categories: similarity search/alignment, similarity search - Software type(s): website - tool
Sequerome is a web based Java tool that acts as a front-end to BLAST queries and provides simplified access to web-distributed resources for protein and nucleic acid analysis. It provides a web-based sequence profiling tool for integrating the results of a BLAST sequence-alignment report with external research tools and servers that perform advanced sequence manipulations, and allowing the user to record the steps of such an analysis.
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: 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.
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