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Showing 20 records out of 379 total
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Categories: proteomics, (protein structure) - Software type(s): website - tool
NetSurfP server predicts the surface accessibility and secondary structure of amino acids in an amino acid sequence. The method also simultaneously predicts the reliability for each prediction, in the form of a Z-score. The Z-score is related to the surface prediction, and not the secondary structure.
Categories: proteomics, (protein structure) - Software type(s): website - tool
NetTurnP predicts if an amino acid is located in a Beta-turn or not. Optional, NetTurnP is also able to predict the nine Beta-turn subtypes.
Categories: genomics, (sequence alignment), evolutionary biology - Software type(s): CLI - tool
The Newick Utilities are a set of command-line tools for processing phylogenetic trees. They can process arbitrarily large amounts of data and do not require user interaction, which makes them suitable for automating phylogeny processing tasks.
Categories: proteomics, (protein sequences and identification, function analysis) - Software type(s): website - database
neXtProt is an innovative knowledge platform dedicated to human proteins. This resource contains a wealth of high-quality data on all the human proteins that are produced by the 20'000 protein-coding genes found in the human genome. The content of neXtProt is continuously extended so as to provide many more carefully selected data sets and analysis tools.
Categories: evolutionary biology - Software type(s): website - tool
Nextstrain is an open-source project to harness the scientific and public health potential of pathogen genome data. We provide a continually-updated view of publicly available data alongside powerful analytic and visualization tools for use by the community. Our goal is to aid epidemiological understanding and improve outbreak response.
Categories: IT infrastructure - Software type(s): CLI - tool
Nfswatch is a command-line tool for monitoring NFS traffic. Nfswatch can capture and analyze the NFS packets on a particular network interface or on all interfaces.
keywords:
Categories: proteomics, (protein modifications) - Software type(s): website - tool
Prediction of N-terminal N-myristoylation of proteins
Categories: proteomics, (protein structure) - Software type(s): website - tool
NQ-Flipper recognizes unfavorable rotamers of Asn and Gln residues in protein structures and corrects them.
Categories: glycomics - Software type(s): website - tool
Built from a model of the de novo biosynthesis of O-linked glycans, O-Glycologue is a method for generating networks of reactions based on the activities of a set of 26 human glycosyltransferase and sulfotransferase enzymes. The effects of enzyme knock-outs on the network can be predicted, and also the enzymes required to produce a given O-glycan.
Categories: genomics, (characterisation/annotation), evolutionary biology - Software type(s): website, CLI, API - database/tool
OMA is a project that aims to identify orthologs among publicly available, complete genomes. With many hundreds of genomes analyzed to date, OMA is one of the largest projects of its kind.
Categories: proteomics - Software type(s): website - tool
One to Three converts single letter translations to three letter translations.
Categories: genomics, (characterisation/annotation) - Software type(s): website - database
The OpenFlu database (OpenFluDB) is part of a collaborative effort to share observations on the evolution of Influenza virus in both animals and humans. It contains genomic and protein sequences as well as epidemiological data from more than 25'000 isolates.
Categories: proteomics, (protein structure), structure analysis, biophysics - Software type(s): CLI, GUI, library - tool
The OpenStructure library project aims to provide an open-source, modular, flexible, molecular modelling and visualization environment. It is targeted at interested users and method developers in the field of structural bioinformatics. Its cleanly designed API available in both Python an C++ provides a command line interface for batch processing as well as a graphical user interface fully scriptable in Python.
Categories: genomics, (characterisation/annotation), evolutionary biology - Software type(s): website - database
Catalog of eukaryotic orthologous protein-coding genes. OrthoDB explicitly delineates orthologs at each radiation along the species phylogeny. Available protein descriptors, together with Gene Ontology and InterPro attributes, serve to provide general descriptive annotations of the orthologous groups, and facilitate comprehensive database querying. Data sources include proteomes from arthropods, fungi, vertebrates and basal metazoans.
Categories: genomics - Software type(s): website - tool
PACMAN generates publication quality images of methylated motifs counts, locations and non-methylated locations, on one or both strands of the DNA. The user can apply several filters on the gff data to avoid bad quality modifications or low coverage, for example. The optional filters are the IPDratio, the coverage and the identification quality value (idqv). This web page requires upload of a bacterial full or draft genome, together with the motifs.gff file of a PacBio sequencing analysis.
keywords: DNA methylation
Categories: proteomics, (sequence sites, features and motifs) - Software type(s): website - tool
Paircoil2 predicts the parallel coiled coil fold from sequence using pairwise residue probabilities with the Paircoil algorithm and an updated coiled coil database. Paircoil2 shows improved performance over Paircoil and other coiled-coil prediction algorithms.
Categories: proteomics - Software type(s): website - tool
PATS identifies amino acid sequences that are potentially targeted to the apicoplast matrix of Plasmodium falciparum. Secondary analysis of candidate sequences is required for confirmation.
Categories: proteomics, (sequence sites, features and motifs) - Software type(s): website - tool
PattInProt allows to scan a protein database of one or several sequences for one or several patterns written in PROSITE syntax. The tool allows to specify an allowed number of mismatches or a similarity threshold towards the pattern.
Categories: proteomics - Software type(s): website - database
PaxDb contains estimated abundance values for a large number of proteins in several different species. Furthermore, it contains information about inter-species variation of protein abundances.
Categories: proteomics, (protein structure, protein interactions) - Software type(s): website - tool
PDBePISA is an interactive tool for the exploration of macromolecular (protein, DNA/RNA and ligand) interfaces, prediction of probable quaternary structures (assemblies), database searches of structurally similar interfaces and assemblies, as well as searches on various assembly and PDB entry parameters.
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