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Showing 20 records out of 363 total
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Categories: proteomics, (function analysis), systems biology - Software type(s): website, databases files - database/tool allows to access, analyse and manipulate genome-scale metabolic networks as well as biochemical pathways. It consistently integrates data from various public resources and makes the data accessible in a standardized format using a common namespace. Models can be interactively compared, analysed (e.g. detection of dead-end metabolites/reactions, flux balance analysis or simulation of reaction/gene knockouts), manipulated and exported. Users can upload their own metabolic models.
Categories: proteomics, (proteomics experiment) - Software type(s): website - database
MIAPEGelDB helps end-users to write MIAPE documents (minimum information to report when describing or publishing a proteomics experiment), through a self-documenting web interface. The produced documents are stored in a database, and thus remain easily accessible by anybody through a stable URL unique for each document.
Categories: genomics - Software type(s): website - tool
miRmap provides comprehensive prediction of microRNA target repression strength. MicroRNAs, or miRNAs, post-transcriptionally repress the expression of protein-coding genes. Our resource enables to search precompiled and predict online miRNA targets with miRmap.
Categories: genomics, (characterisation/annotation), evolutionary biology - Software type(s): website - database
miROrtho contains predictions of precursor miRNA genes covering many animal genomes combining evidence from sequence homology and Support Vector Machine classifiers. We provide both consistent extrapolation of already known miRBase families and novel miRNA predictions by our SVM and orthology pipeline.
Categories: proteomics, (function analysis) - Software type(s): website - tool
MitoFates predicts mitochondrial presequence, a cleavable localization signal located in N-terminal, and its cleaved position.
Categories: proteomics, (protein modifications) - Software type(s): website - tool
MitoProt calculates the N-terminal protein region that can support a mitochondrial targeting sequence and the cleavage site.
Categories: evolutionary biology - Software type(s): CLI - tool
MLtree is a software to compute maximum likelihood optimization of models of character evolution (either DNA or phenotypic ones) along the branches of a phylogenetic tree. It is assuming that the phylogenetic tree is known.
Categories: evolutionary biology - Software type(s): website - tool
MLTreeMap is a tool that employs full maximum likelihood to give insights into phylogenetic and functional properties of metagenomes and the underlying microbial communities. It does so by detecting and phylotyping a series of relevant marker genes on the submitted DNA fragments. Among these genes are protein coding phylogenetic markers, SSU rRNA genes and markers for important functional pathways. MLTreeMap is available as a web-server and as a stand-alone version.
Categories: proteomics, (protein structure) - Software type(s): GUI - tool
MolTalk is a computational environment (programming library with an integrated scripting language) for doing structural bioinformatics. It interprets PDB formatted files and creates an object representation of the structure-chain-residue-atom hierarchy.
keywords: tertiary structure
Categories: proteomics, (protein structure), imaging - Software type(s): website - tool
MovieMaker is a web server that allows short (~10 sec), downloadable movies to be generated of protein dynamics. It accepts PDB files or PDB accession numbers as input and automatically outputs colorful animations covering a wide range of protein motions and other dynamic processes.
Categories: proteomics, (proteomics experiment), imaging - Software type(s): website, GUI - tool
MSight: An image analysis software for liquid chromatography-mass spectrometry. MSight is a tool specifically developed for the representation of mass spectra along with data from a separation step. It provides simple ways to navigate through very large volumes of data, with the ability to display small regions for closer scrutiny.
Categories: proteomics, (similarity search/alignment), genomics, (sequence alignment) - Software type(s): website - tool
Multiple sequence alignment with hierarchical clustering
Categories: proteomics, (sequence sites, features and motifs) - Software type(s): website - tool
The MultiCoil program predicts the location of coiled-coil regions in amino acid sequences and classifies the predictions as dimeric or trimeric. The method is based on the PairCoil algorithm. To analyze your own sequences with MultiCoil, you can either use the web interface or download the program.
Categories: proteomics, (similarity search/alignment), genomics, (sequence alignment) - Software type(s): website - tool
Multiple alignment server
keywords: sequence alignment
Categories: proteomics, (sequence sites, features and motifs) - Software type(s): website - tool
Image Creator for linear (multi) domain views
keywords: protein domain
Categories: proteomics, (sequence sites, features and motifs, similarity search/alignment) - Software type(s): website - database/tool
Hits is a free database devoted to protein domains. It is also a collection of tools for the investigation of the relationships between protein sequences and motifs described on them. These motifs are defined by an heterogeneous collection of predictors, which currently includes regular expressions, generalized profiles and hidden Markov models.
Categories: proteomics, (protein modifications) - Software type(s): website - tool
Predict N-terminal myristoylation of proteins by neural networks. Myristoylator uses ensembles of neural networks, in order to learn to discriminate positive and negative sequences for N-myristoylation.
Categories: proteomics, (proteomics experiment), glycomics - Software type(s): CLI, API - tool
MzJava is an open-source Java library for the analysis of mass spectrometry data. It provides algorithms and data structures for processing mass spectra and their associated biological molecules, such as small molecules, glycans, proteins, and peptides with post-translational modifications. MzJava includes methods to perform mass calculation, protein digestion, peptide and glycan fragmentation, MS/MS signal processing, and scoring for spectra-spectra and peptide/glycan-spectra matches.
Categories: proteomics, (protein modifications) - Software type(s): website - tool
NetAcet predicts substrates of N-acetyltransferase A (NatA). The method was trained on yeast data but it obtains similar performance values on mammalian substrates acetylated by NatA orthologs.
Categories: proteomics, (protein modifications), glycomics - Software type(s): website - tool
Neural network predictions of C-mannosylation sites in mammalian proteins.
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