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Showing 20 records out of 359 total
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Categories: proteomics, (protein structure), structure analysis, biophysics - Software type(s): website - tool
Estimating the quality of predicted structural models is a crucial step in homology modeling. Scoring functions analyze different structural features of the protein models in order to generate a quality estimate. QMEAN consists of four statistical potential terms (two non-bonded interaction terms, a torsion angle term and a solvation term) and two components describing the agreement between predicted and observed secondary structure and solvent accessibility.
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: proteomics, (proteomics experiment, protein modifications) - Software type(s): CLI, GUI - tool
QuickMod is a spectral library search based MSMS data analysis tool, designed to identify modified peptides. The QuickMod algorithm assumes that the precursor mass difference between a query spectrum and a candidate library spectrum can be explained by a modification. Based on this assumption the two spectra are aligned and the fit of the spectral alignment is assigned a similarity score. In a second step the most likely attachment position of the modification is determined.
Categories: proteomics, (sequence sites, features and motifs) - Software type(s): website - tool
RADAR stands for Rapid Automatic Detection and Alignment of Repeats in protein sequences. Many large proteins have evolved by internal duplication and many internal sequence repeats correspond to functional and structural units. Radar is uses an automatic algorithm, for segmenting your query sequence into repeats, it identifies short composition biased as well as gapped approximate repeats and complex repeat architectures involving many different types of repeats in your query sequence.
Categories: proteomics - Software type(s): website - tool
Random protein sequence generator
Categories: proteomics - Software type(s): website - tool
This server predicts peptide binders to MHCI and MHCII molecules from protein sequence/s or sequence alignments using Position Specific Scoring Matrices (PSSMs). In addition, it predicts those MHCI ligands whose C-terminal end is likely to be the result of proteasomal cleavage. A detailed explanation of the method can be found here.
Categories: proteomics, (protein structure), imaging - Software type(s): GUI - tool
RasMol is a program for molecular graphics visualization.
Categories: proteomics, evolutionary biology - Software type(s): website - tool
RAxML (Randomized Axelerated Maximum Likelihood) is a program for sequential and parallel Maximum Likelihood based inference of large phylogenetic trees. It has originally been derived from fastDNAml which in turn was derived from Joe Felsentein's dnaml which is part of the PHYLIP package.
Categories: evolutionary biology - Software type(s): website, CLI - tool
REALPHY - The Reference sequence Alignment based Phylogeny builder is a free online pipeline that can infer phylogenetic trees from whole genome sequence data. The user only has to provide genome sequences in FASTA, GenBank or FASTQ formats. From these sequences phylogenetic trees are inferred via PhyML. The alignments, tree files and information on SNPs and deleted sites will be available for download after the analysis is finished.
Categories: proteomics, (sequence sites, features and motifs) - Software type(s): website - tool
Protein search for repeats, using a collection of repeat families
Categories: proteomics, (sequence sites, features and motifs) - Software type(s): website - tool
REPRO is able to recognise distant repeats in a single query sequence. The technique relies on a variation of the Smith-Waterman local alignment strategy to find non-overlapping top-scoring local alignments, followed by a graph-based iterative clustering procedure to delineate the repeat set(s) based on consistency of the pairwise top-alignments.
Categories: proteomics, genomics - Software type(s): website - tool
This tool converts DNA to RNA to protein, and reverse transcript RNA to DNA.
keywords: translation
Categories: protein sequences and identification, genomics - Software type(s): website - tool
Accepts a protein sequence as input and uses a codon usage table to generate a DNA sequence representing the most likely non-degenerate coding sequence. A consensus sequence derived from all the possible codons for each amino acid is also returned.
keywords: translation
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.
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