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Showing 20 records out of 379 total
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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.
Categories: evolutionary biology - Software type(s): website - tool
Compilation of links to 390 phylogeny packages and about 50 free web servers, arranged by several criteria.
Categories: evolutionary biology - Software type(s): website - tool is a free, simple to use web service dedicated to reconstructing and analysing phylogenetic relationships between molecular sequences. It runs and connects various bioinformatics programs to reconstruct a robust phylogenetic tree from a set of sequences.
Categories: genomics, (sequence alignment, similarity search), systems biology - Software type(s): website, CLI, GUI - tool
Phylogibbs is an algorithm for discovering regulatory sites in a collection of DNA sequences, including multiple alignments of orthologous sequences from related organisms.The algorithm uses a Gibbs sampling strategy, takes the phylogenetic relationships of the input sequences rigorously into account, and assigns realistic posterior probabilities to reported sites using a novel annealing+tracking strategy.
Categories: proteomics, (protein structure) - Software type(s): website - tool
As with Phyre, the new system is designed around the idea that you have a protein sequence/gene and want to predict its three-dimensional (3D) structure. Whereas Phyre used a profile-profile alignment algorithm, Phyre2 uses the alignment of hidden Markov models via HHsearch to significantly improve accuracy of alignment and detection rate.
Categories: proteomics, (protein structure), structure analysis - Software type(s): website - database
PhyreRisk is a dynamic web application developed to enable the exploration and mapping of genetic variants onto experimental and predicted structures of proteins and protein complexes. PhyreRisk integrates data from several public domain and in-house databases with information about diseases, genetic variation, biological pathways and protein structure and then facilitate the informed analysis by a wide community of users throughout the world.
Categories: proteomics, (proteomics experiment) - Software type(s): website, GUI - tool
A tool to visualize theoretical distributions of peptide pI on a given pH range and generate fractions with similar peptide frequencies
Categories: transcriptomics - Software type(s): CLI - tool
The Ping-Pong Algorithm (PPA) is a method for integrating tabular data sets that share a common dimension. A typical example for this is gene expression across a set of tissues and drug-response data for the same tissues. The PPA finds co-modules in the two data sets, i.e. genes that are co-expressed in some tissues that have similar responses to a subset of the drugs. The co-modules can overlap; the PPA is efficient and scales well to large data sets. A Matlab implementation is provided.
Categories: proteomics, (sequence sites, features and motifs, similarity search/alignment) - Software type(s): website - tool
Protein sequence logos using relative entropy.
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