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Showing 20 records out of 379 total
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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: structure analysis - Software type(s): website - tool
rBAN (retroBiosynthetic Analysis of Nonribosomal peptides) is a computational tool designed to predict the monomeric graph of NRPs from their atomic structure in SMILES format. This prediction is achieved through the in-silico fragmentation of a chemical structure and matching the resulting fragments against the monomers of Norine for identification.
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.
Categories: evolutionary biology - Software type(s): website, databases files - 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: 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.
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