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Showing 20 records out of 375 total
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Categories: glycomics - Software type(s): website - tool
Glynsight is a web interface to upload, visualize and interactively compare glycan expression profiles. The tool can process N- or O-linked glycan expression data.
Categories: glycomics - Software type(s): website - tool
GlyS3 matches any substructure such as glycan determinants to a large collection of structures recorded in Glyconnect or SugarBind.
Categories: glycomics - Software type(s): website - database
GlyTouCan is the international glycan structure repository. It is an uncurated registry for glycan structures that assigns globally unique accession numbers to any glycan independent of the level of information provided by the experimental method used to identify the structure(s).
Categories: genomics, (characterisation/annotation) - Software type(s): CLI - tool
Gaussian Mixture Model (GMM) detects copy number variation from the distribution of copy number ratios. From the data, it will fit one component for each of the following copy number states: deletion, copy-neutral, 1 and 2 additional copy; with a constraint on the difference between the mixture means. Then for a given individual, it will determine the probabilities for each copy number state and compute the expected copy number (dosage).
Categories: proteomics, (protein structure) - Software type(s): website - tool
Protein secondary structure prediction
Categories: proteomics, (protein modifications) - Software type(s): website - tool
Identification of GPI-anchor signals by a Kohonen self organizing map
Categories: proteomics, (function analysis) - Software type(s): website - tool
GPMAW lite is a protein bioinformatics tool to perform basic bioinformatics calculations on any protein amino acid sequence, including predicted molecular weight, molar absorbance and extinction coefficient, isoelectric point and hydrophobicity index, as well as amino acid composition and protease digest.
Categories: proteomics, (protein modifications) - Software type(s): website - tool
Computational prediction of phosphorylation sites with their cognate protein kinases (PKs) is greatly helpful for further experimental design. GPS could predict kinase-specific phosphorylation sites for 408 human PKs in hierarchy.
Categories: protein sequences and identification, genomics - Software type(s): website - tool
Differences in codon usage preference among organisms lead to a variety of problems concerning heterologous gene expression but can be overcome by rational gene design and gene synthesis. The gcua tool displays the codon quality either in codon usage frequency values or relative adaptiveness values
Categories: proteomics, (protein sequences and identification, function analysis, sequence sites, features and motifs) - Software type(s): website - database/tool
HAMAP is a system for the classification and annotation of protein sequences. It consists of a collection of manually curated family profiles for protein classification, and associated, manually created annotation rules that specify annotations that apply to family members. HAMAP is applied to bacterial, archaeal and eukaryotic proteins and used to annotate records in UniProtKB via UniProt's automatic annotation pipeline.
Categories: proteomics, (sequence sites, features and motifs) - Software type(s): website - tool
Scan several protein sequences or a whole genome (all ORFs) against HAMAP family profiles. Sequences that match HAMAP profiles will be annotated in the UniProtKB format by the associated annotation rules.
Categories: proteomics - Software type(s): website - tool
The HCA method is based on the use of a bidimensional plot, called the HCA plot. The bidimensional plot is associated with an alpha helicoidal pitch (3.6 residue/turn, connectivity distance of 4) which has been shown to offer the best correspondence between clusters and regular secondary structures. Examination of the HCA plot of a protein sequence allow to easily identify globular regions from non globular ones and, in globular regions, to identify secondary structures.
Categories: proteomics, (sequence sites, features and motifs) - Software type(s): website - tool
HeliQuest calculates from the amino acid sequence of a helix (??-helix, 3-10 helix, 3-11 helix or ?? helix) its physicochemical properties and amino acid composition and uses the results to screen any databank in order to identify protein segments possessing similar features.
Categories: proteomics, (protein structure) - Software type(s): website - tool
Homology detection & structure prediction by HMM-HMM comparison
Categories: proteomics, (protein modifications) - Software type(s): website - tool
Prediction of transmembranes helices and topology of proteins.
Categories: proteomics, (protein structure) - Software type(s): website - tool
Helical TransMembrane Segment Rotational Angle Prediction
Categories: proteomics, (proteomics experiment), imaging - Software type(s): website, GUI - tool
Melanie offers a unique and flexible interface for the comprehensive visualization, exploration and analysis of 2D gel data. It provides powerful and innovative solutions to shorten the path from data acquisition to protein information, both for conventional 2-DE and DIGE (Fluorescence Difference Gel Electrophoresis) gels.
Categories: genomics, (characterisation/annotation), evolutionary biology - Software type(s): website - database
A simple access point to view gene family assignments, annotations and phylogenetic data for insect immune-related genes and gene families.
Categories: proteomics, (proteomics experiment) - Software type(s): website - tool
InsPecT is an MS/MS database search tool, with an emphasis on efficiently and confidently identifying modified peptides. It includes special scoring models for phosphorylation which allow for increased accuracy. In addition, InsPecT implements the MS-Alignment algorithm for discovery of unanticipated modifications in blind mode.
Categories: proteomics, (sequence sites, features and motifs) - Software type(s): website - tool
InterProScan is a tool that combines different protein signature recognition methods into one resource. The number of signature databases and their associated scanning tools, as well as the further refinement procedures, increases the complexity of the problem.
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