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Showing 20 records out of 375 total
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Categories: proteomics, (protein structure), imaging - Software type(s): GUI - tool
MarvinSpace is a Java-based software for visualization, modeling and interactive rendering
Categories: proteomics, (proteomics experiment) - Software type(s): website - tool
Mascot is a powerful search engine which uses mass spectrometry data to identify proteins from primary sequence databases. Mascot integrates all of the proven methods of searching: Peptide Mass Fingerprint (the only experimental data are peptide mass values), Sequence Query (peptide mass data are combined with amino acid sequence and composition information), MS/MS Ion Search using uninterpreted MS/MS data from one or more peptides.
Categories: proteomics, (function analysis), glycomics - Software type(s): website - database
MatrixDB is a curated database of interactions between extracellular matrix proteins, proteoglycans and polysaccharides. It mainly focuses on protein-glycosaminoglycan (GAG) interactions, as GAGs are complex and abundant polysaccharides in the ECM and at the cell surface, where they play key roles in adhesion and signaling.
Categories: similarity search/alignment, sequence alignment - Software type(s): website - tool
The presence of gaps in an alignment of nucleotide or protein sequences is often an inconvenience for bioinformatical studies. MaxAlign maximizes the number of characters that are present in gap-free columns. It can be used prior to any phylogenetic analysis as well as in other situations where this form of alignment clean up is useful, such as the presence of badly aligned or truncated sequences.
keywords: alignment analysis
Categories: proteomics - Software type(s): website - tool
Ranking the biomedical literature according to a selected topic.
Categories: proteomics, (protein structure) - Software type(s): website, GUI - tool
Disordered proteins or protein segments lack a folded tertiary structure. They are thought to be intrinsically disordered regions providing essential biological functions. MeDor is a metaserver for predicting protein disorder
Categories: proteomics, (function analysis), systems biology - Software type(s): website, databases files - database/tool
MetaNetX.org 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, (protein structure), structure analysis - Software type(s): website - tool
Missense3D predicts the structural changes introduced by an amino acid substitution and is applicable to analyse both PDB coordinates and homology-predicted structures.
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: genomics, population genetics, transcriptomics - Software type(s): CLI - tool
The mOTUs tool uses phylogenetic marker gene (MG)-based operational taxonomic units (mOTUs) to profile microorganisms at species-level resolution when using metagenomic data as input. Since the MGs represent housekeeping genes, mOTUs can also be used to profile transcriptionally active community members when using metatranscriptomic data as input. Furthermore, MG-based SNV profiling provides an efficient alternative to using whole genome sequences to compare microbial strain populations.
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
keywords:
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