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Showing 20 records out of 371 total
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Categories: proteomics, (protein structure) - Software type(s): website - tool
TopSearch is a new powerful gateway to protein structures and their structural relationships. Given a query structure the search engine instantly returns a list of known protein structures sorted by structural similarity. TopSearch operates on three structural levels: chains, biological assemblies and quaternary structures, and asymmetric units.
Categories: proteomics, (protein sequences and identification), genomics, transcriptomics - Software type(s): website - tool
Translation of a nucleotide (DNA/RNA) sequence to a protein sequence.
Categories: genomics, (characterisation/annotation), population genetics - Software type(s): GUI - tool
TRiFLe is a program for simulating TRFs and identifying species by TRF profiling
Categories: genomics, (characterisation/annotation), transcriptomics - Software type(s): website, CLI - tool
The transcriptome analyser project aims to provide tools to determine and document all the transcribed parts of a genome. The transcribed parts are defined by analysing experimental evidence, like expressed sequence tags (EST) and other mRNA sequences.
Categories: proteomics, (sequence sites, features and motifs) - Software type(s): website - tool
TRUST is a method for ab-initio determination of internal repeats in proteins. The high sensitivity and accuracy of the method is achieved by exploiting the concept of transitivity of alignments.
Categories: glycomics - Software type(s): website - database
UniCarb-DB stores data and information on glycan structures and associated fragment data characterised by LC-MS/MS strategies. It is annotated with high-quality datasets.
Categories: glycomics - Software type(s): website - database
UniCarbKB is a curated and annotated glycan database which curates information from the scientific literature on glycoprotein derived glycan structures. It includes data previously available from GlycoSuiteDB.
Categories: proteomics, glycomics - Software type(s): website - database
UniLectin is a platform integrating information regarding non-enzymatic carbohydrate-binding proteins usually referred to as lectins with the prospect of building and refining a structural and functional classification of these proteins. It includes the reference Lectin3D a database of 3D structures curated from the PDB.
Categories: proteomics - Software type(s): website - database
UniParc is a comprehensive and non-redundant database provided by the UniProt Consortium that contains most of the publicly available protein sequences. Proteins may exist in different source databases and in multiple copies in the same database. UniParc avoids such redundancy by storing each unique sequence only once and giving it a stable and unique identifier allowing to identify the same protein from different source databases. UniParc contains only protein sequences.
Categories: proteomics, (protein sequences and identification, function analysis, similarity search/alignment) - Software type(s): website - database
The UniProt Knowledgebase (UniProtKB) is produced by the UniProt consortium and is the central hub for the collection of functional information on proteins with accurate, consistent and rich annotation. It consists of: UniProtKB/Swiss-Prot (manually-annotated records and curator-evaluated computational analysis) and UniProtKB/TrEMBL (computationally analyzed records awaiting manual annotation).
Categories: proteomics, (protein sequences and identification, function analysis, protein modifications, protein interactions) - Software type(s): website - database
UniProtKB/Swiss-Prot is the manually annotated component of UniProtKB (produced by the UniProt consortium). It contains manually-annotated (reviewed) records with information extracted from the literature and curator-evaluated computational analysis.
Categories: proteomics, (protein sequences and identification) - Software type(s): website, databases files - database
The UniRef databases provide clustered sets of sequences from UniProt Knowledgebase (including splice variants and isoforms) and selected UniParc records, in order to obtain complete coverage of sequence space at several resolutions while hiding redundant sequences (but not their descriptions) from view.
Categories: genomics, (sequence alignment), population genetics - Software type(s): CLI - tool
V-pipe is a bioinformatics pipeline for the analysis of next-generation sequencing (NGS) data derived from intra-host viral populations.
Categories: proteomics, (protein sequences and identification) - Software type(s): website - database
VenomZone is a free web resource that provides information on venoms from six animal taxa (snakes, scorpions, spiders, cone snails, sea anemones and insects), as well as on their targets. Information can be browsed through pages on taxonomy, activity and venom protein families and all these pages link to related venom/toxin protein information from the manually curated UniProtKB/Swiss-Prot database.
Categories: proteomics, (protein sequences and identification) - Software type(s): website - database
ViralZone is a web resource for all viral genus and families, providing general molecular and epidemiological informations, along with virion and genome figures. Each virus or family page gives an easy access to UniProtKB/Swiss-Prot viral protein entries.
keywords: pathogen
Categories: proteomics, IT infrastructure - Software type(s): website, CLI - tool
Vital-IT is an innovative life science informatics initiative providing computational resources, consultancy and training to connect fundamental and applied research.
Categories: proteomics, (protein structure), imaging - Software type(s): GUI - tool
VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running MacOS X, Unix, or Windows, is distributed free of charge, and includes source code.
Categories: proteomics, (sequence sites, features and motifs, similarity search/alignment), genomics, (sequence alignment) - Software type(s): website - tool
Sequence logos are a graphical representation of an amino acid or nucleic acid multiple sequence alignment. Each logo consists of stacks of symbols, one stack for each position in the sequence. The overall height of the stack indicates the sequence conservation at that position, while the height of symbols within the stack indicates the relative frequency of each amino or nucleic acid at that position.
Categories: proteomics, (sequence sites, features and motifs) - Software type(s): website, GUI - tool
WeStBESel is a tool to help selecting the most relevant B-cell epitopes according to the user needs (i.e. vaccines, diagnostic test, etc). We use a mixed approach by combining : physico-chemical property-based approaches (conservation intra and interspecies, PTM, hydrophobicity, solvent accessibility, disorder and mutations), sliding windows algorithm paired with five of the best B-cell epitopes prediction tools (ABCPred, AAP, BCPred, BepiPred, SVMTrip).
Categories: proteomics, (protein structure) - Software type(s): website - tool
WHAT IF is a versatile molecular modelling package that is specialized on working with proteins and the molecules in their environment like water, ligands, nucleic acids, etc.
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