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Showing 20 records out of 359 total
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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, (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.
Categories: proteomics, (protein structure) - Software type(s): website - tool
Disordered proteins or protein segments lack a folded tertiary structure. They are thought to be intrinsically disordered regions providing essential biological functions, so predicting such disorder should help understand protein functions.
Categories: proteomics, (protein structure) - Software type(s): website - tool
The PoPMuSiC program is a tool for the computer-aided design of mutant proteins with controlled stability properties. It evaluates the changes in stability of a given protein or peptide under single-site mutations, on the basis of the protein's structure.
Categories: proteomics, (function analysis) - Software type(s): website - tool
The PoPS project is a set of computational tools for investigating protease specificity. The main PoPS program allows users to model and profile protease specificity and predict substrate cleavage. Other tools are available to search for substrates within proteomes (protein databases for organisms), and create simple matrix models of specificity from experimental data.
Categories: proteomics - Software type(s): website - tool
Protein Secondary Structure Prediction
Categories: proteomics, (sequence sites, features and motifs) - Software type(s): website - tool
Search your query sequence for protein motifs, rapidly compare your query protein sequence against all patterns stored in the PROSITE pattern database and determine what the function of an uncharacterised protein is. This tool requires a protein sequence as input, but DNA/RNA may be translated into a protein sequence using transeq and then queried. Allows a graphical output.
Categories: proteomics, (sequence sites, features and motifs) - Software type(s): website - tool
An important problem in sequence analysis is to find patterns matching sets or subsets of sequences. This tool allows the user to discover patterns conserved in sets of unaligned protein sequences. The user can specify what kind of patterns should be searched for, and how many sequences should match a pattern to be reported. The patterns are reported using PROSITE syntax.
Categories: proteomics, (sequence sites, features and motifs) - Software type(s): website - tool
An important problem in sequence analysis is to find patterns matching sets or subsets of sequences.This tool allows the user to search for patterns conserved in sets of unaligned protein sequences. The user can specify what kind of patterns should be searched for, and how many sequences should match a pattern to be reported.
Categories: proteomics, (function analysis, sequence sites, features and motifs, protein modifications, protein interactions) - Software type(s): website - tool
PredictProtein integrates feature prediction for secondary structure, solvent accessibility, transmembrane helices, globular regions, coiled-coil regions, structural switch regions, B-values, disorder regions, intra-residue contacts, protein-protein and protein-DNA binding sites, sub-cellular localization, domain boundaries, beta-barrels, cysteine bonds, metal binding sites and disulphide bridges.
Categories: proteomics, (protein modifications) - Software type(s): website - tool
Predotar was designed for systematic screening of large batches of proteins for identifying putative targeting sequences, and recognizes the N-terminal targeting sequences of classically targeted precursor proteins. It provides a probability estimate as to whether the sequence contains a mitochondrial, plastid or ER targeting sequence.
Categories: proteomics, (protein modifications) - Software type(s): website - tool
The prenylation prediction suite (PrePS) combines three predictors for protein CaaX farnesylation, CaaX geranylgeranylation and Rab geranylgeranylation in one webinterface. The predictors aim to model the substrate-enzyme interactions based on refinement of the recognition motifs for each of the prenyltransferases.
Categories: proteomics - Software type(s): library - tool
A package (R, S+) to visualize, smooth and compare receiver operating characteristic (ROC curves)
keywords:
Categories: proteomics, (protein structure) - Software type(s): website - tool
PROCHECK checks the stereochemical quality of a protein structure, producing a number of PostScript plots analysing its overall and residue-by-residue geometry. It includes PROCHECK-NMR for checking the quality of structures solved by NMR.
Categories: proteomics, (sequence sites, features and motifs) - Software type(s): website - tool
ProDom is a protein domain family database constructed automatically by clustering homologous segments. Compare your sequence with ProDom by running a Blast-P or Blast-X search against: the consensus sequence provided with the ProDom families or the multiple alignments provided with each ProDom family. ProDom-CG (Complete Genomes) and ProDom-SG (Structural Genomics Candidate Search) can also be searched.
Categories: proteomics, (protein structure) - Software type(s): website - tool
Secondary Structure Prediction System
Categories: proteomics, (proteomics experiment) - Software type(s): website - tool
Tool for searching protein sequence collections with peptide mass maps. A Bayesian algorithm is used to rank the protein sequences in the database according to their probability of producing the peptide map.
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