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Showing 20 records out of 365 total
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Categories: proteomics, (sequence sites, features and motifs) - Software type(s): website - tool
This program delineates coiled-coil domains in otherwise globular proteins, such as the leucine zipper domains in transcriptional regulators, and to predict regions of discontinuity within coiled-coil structures, such as the hinge region in myosin.
Categories: proteomics, (protein structure), genomics, (characterisation/annotation), structure analysis - Software type(s): website, CLI - tool
COILS is a program that compares a sequence to a database of known parallel two-stranded coiled-coils and derives a similarity score. By comparing this score to the distribution of scores in globular and coiled-coil proteins, the program then calculates the probability that the sequence will adopt a coiled-coil conformation.
Categories: proteomics - Software type(s): website - tool
Color Protein Sequence.
keywords:
Categories: proteomics, (function analysis) - Software type(s): website - tool
Compute the theoretical pI (isoelectric point) and Mw (molecular weight) for a list of UniProt Knowledgebase (Swiss-Prot or TrEMBL) entries or for user entered sequences
Categories: proteomics, (protein structure) - Software type(s): website - tool
CPHmodels 3.2 is a protein homology modeling server. The template recognition is based on profile-profile alignment guided by secondary structure and exposure predictions
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: glycomics - Software type(s): website - database
CSDB covers information on structures and taxonomy of natural carbohydrates published in the literature and mostly resolved by nuclear magnetic resonance (NMR). CSDB is composed of two parts: Bacterial & Archeal (BCSDB) and Plant & Fungal (PFCSDB). The databases can be queried together or separately with multiple criteria. Supporting tools for NMR data analysis and prediction as well as statistical analysis of glycomes in taxa are included.
Categories: proteomics, (protein modifications) - Software type(s): website - tool
Palmitoylation will enhance the surface hydrophobicity and membrane affinity of protein substrates, and play important roles in modulating proteins' trafficking and stability. After manual collection of the experimentally verified palmitoylation sites from scientific literature, we could get training data containing 439 palmitoylation sites from 194 distinct proteins, used to train the CSS-Palm program.
Categories: evolutionary biology, population genetics - Software type(s): CLI - tool
Continuous time conjunctive Bayesian networks (ct-cbn) are a family of graphical models describing the accumulation of mutations under order constraints. The software allows for the estimation of the network from cross-sectional data, such as mutation profiles of cancer or HIV patients.
keywords: Bayesian network
Categories: proteomics, (protein modifications) - Software type(s): website - tool
DAS (Dense Alignment Surface) is based on low-stringency dot-plots of the query sequence against a set of library sequences - non-homologous membrane proteins - using a previously derived, special scoring matrix. The method provides a high precision hyrdophobicity profile for the query from which the location of the potential transmembrane segments can be obtained. The novelty of the DAS-TMfilter algorithm is a second prediction cycle to predict TM segments in the sequences of the TM-library.
Categories: proteomics, (protein sequences and identification, similarity search/alignment), genomics, (sequence alignment) - Software type(s): website - tool
Redundancy reduction in a set of aligned or unaligned sequences
Categories: evolutionary biology - Software type(s): website - tool
This tool creates a dendrogram from (a) a set of variables or (b) from a similarity matrix. The program calculates a similarity matrix (only for option a), transforms similarity coefficients into distances and makes a clustering using the Unweighted Pair Group Method with Arithmetic mean (UPGMA) algorithm.
Categories: similarity search/alignment, sequence alignment - Software type(s): website - tool
While standard alignment methods rely on comparing single residues and imposing gap penalties, DIALIGN constructs pairwise and multiple alignments by comparing entire segments of the sequences. No gap penalty is used. This approach can be used for both global and local alignment, but it is particularly successful in situations where sequences share only local homologies.
keywords: sequence alignment
Categories: proteomics, (protein modifications) - Software type(s): website - tool
Neural network predictions for GlcNAc O-glycosylation sites in Dictyostelium discoideum proteins.
Categories: proteomics, (protein structure) - Software type(s): website - tool
Disordered proteins or protein segments lack a folded tertiary structure. They are thought to be intrinsically disordered regions providing essential biological functions. DisEMBL is a tool for prediction of disordered/unstructured regions within a protein sequence.
Categories: proteomics, (protein structure) - Software type(s): website - tool
DLP-SVM is a domain linker predictor. It is composed of three loop-length dependent SVM predictors of domain linkers (SVM-All, SVM-Long and SVM-Short), and SVM-Joint, which combines the results of SVM-Short and SVM-Long into a single consolidated prediction.
Categories: proteomics, (similarity search/alignment) - Software type(s): website - tool
Diagonal plots to graphically compare of biological sequences and identify regions of close similarity
keywords: sequence alignment
Categories: glycomics - Software type(s): website - tool
DrawGlycan-SNFG uses IUPAC-condensed string inputs to generate glycan and glycopeptide drawings. Bond fragmentation in either glycans or glycopeptides as well as other glycan descriptors can be included.
Categories: evolutionary biology - Software type(s): website - database
The EBI Metagenomics service is an automated pipeline for the analysis and archiving of metagenomic data that aims to provide insights into the phylogenetic diversity as well as the functional and metabolic potential of a sample. You can freely browse all the public data in the repository.
Categories: systems biology - Software type(s): CLI - tool
The efmtool computes elementary flux modes (EFMs) of metabolic networks. It is implemented in Java and has been integrated into MATLAB (see http://www.mathworks.com). EFM computation is a special case of extreme ray enumeration of polyhedral cones.
keywords: metabolism, pathway
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