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Showing 20 records out of 363 total
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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.
Categories: proteomics - Software type(s): website - tool
PepDraw is a tool to draw peptide primary structure and calculate theoretical properties.
Categories: proteomics, (proteomics experiment) - Software type(s): website - tool
PepFrag is a tool for identifying proteins from a collection of sequences that matches a single tandem mass spectrum.
Categories: - Software type(s): - tool
Protein search tool using mass spectrometry data produced by the digestion of a protein to identify a match to a protein from a database.
Categories: proteomics, glycomics - Software type(s): website, GUI - tool
PepSweetener supports the manual annotation of MS data for intact glycopeptides. It displays an interactive map of all theoretical glycopeptides that match the molecular masses of queried precursor ions. Ion matching can be performed in two modes: simple when the search space spans the combination of all tryptic peptides including N-glycosites in the human proteome, and advanced when the search space is custom-built by specifying peptides and glycans.
Categories: proteomics, (function analysis) - Software type(s): website - tool
PeptideCutter predicts potential substrate cleavage sites, cleaved by proteases or chemicals in a given protein sequence. The tool returns the query sequence with the possible cleavage sites mapped on it and/or a table of cleavage site positions.
Categories: proteomics, (protein sequences and identification) - Software type(s): website - tool
Cleave a protein sequence with a chosen enzyme/protease, and computes the masses of the generated peptides. The tool also returns theoretical isoelectric point and mass values for the protein of interest. If desired, PeptideMass can return the mass of peptides known to carry post-translational modifications, and can highlight peptides whose masses may be affected by database conflicts, polymorphisms or splice variants.
Categories: proteomics - Software type(s): website - tool
PEPVAC is a tool aimed to the development of fully covering multi-epitope vaccines against pathogenic organisms based on genome wide predictions of promiscous MHCI-restricted epitopes.
Categories: proteomics, (sequence sites, features and motifs) - Software type(s): website - tool
Scans a sequence against the Pfam protein families database.
Categories: proteomics, (sequence sites, features and motifs, similarity search/alignment) - Software type(s): library - tool
The pftools are a collection of programs to build, calibrate, and search biological sequences with generalized profiles. Generalized profiles are an extension of position specific scoring matrices by including position specific scores for insertions and deletions. They correspond to a matrix representation of a multiple sequence alignment that can be used to search distant homologous sequences and precisely align sequences to the model.
Categories: proteomics, (protein modifications) - Software type(s): website - tool
Prediction of transmembrane topology and signal peptides from the amino acid sequence of a protein.
Categories: evolutionary biology - Software type(s): CLI - tool
PHYLIP is a free package of programs for inferring phylogenies. It is distributed as source code, documentation files, and a number of different types of executables.
Categories: evolutionary biology - Software type(s): website, library - tool is a state of the art tool for visualising and comparing phylogenetic trees on the web. It can be used to view a single tree, or compare the internal structure of two differently inferred trees for the same group of taxons. includes a number of useful features to make the viewing and comparing of even very large trees extremely easy.
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