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ExPASy Proteomics tools  

2010-04-20 11:07:20|  分类: 生信分析软件 |  标签: |举报 |字号 订阅

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http://ca.expasy.org/tools/#proteome

 

You are here: ExPASy CA  > Tools

ExPASy Proteomics tools

The tools marked by ExPASy Proteomics tools - fhqdddddd - 流浪云南 are local to the ExPASy server. The remaining tools are developed and hosted on other servers.

[Protein identification and characterization] [Other proteomics tools] [DNA -> Protein] [Similarity searches] [Pattern and profile searches] [Post-translational modification prediction] [Topology prediction] [Primary structure analysis] [Secondary structure prediction] [Tertiary structure] [Sequence alignment] [Phylogenetic analysis] [Biological text analysis]

Aldente ExPASy Proteomics tools - fhqdddddd - 流浪云南 - Identify proteins with peptide mass fingerprinting data. A new, fast and powerful tool that takes advantage of Hough transformation for spectra recalibration and outlier exclusion. Download the stand-alone version
  • FindMod ExPASy Proteomics tools - fhqdddddd - 流浪云南 - Predict potential protein post-translational modifications and potential single amino acid substitutions in peptides. Experimentally measured peptide masses are compared with the theoretical peptides calculated from a specified Swiss-Prot entry or from a user-entered sequence, and mass differences are used to better characterize the protein of interest.
  • FindPept ExPASy Proteomics tools - fhqdddddd - 流浪云南 - Identify peptides that result from unspecific cleavage of proteins from their experimental masses, taking into account artefactual chemical modifications, post-translational modifications (PTM) and protease autolytic cleavage
  • GlycoMod ExPASy Proteomics tools - fhqdddddd - 流浪云南 - Predict possible oligosaccharide structures that occur on proteins from their experimentally determined masses (can be used for free or derivatized oligosaccharides and for glycopeptides)

  • Mascot - Peptide mass fingerprint from Matrix Science Ltd., London
  • PepMAPPER - Peptide mass fingerprinting tool from UMIST, UK
  • ProFound - Search known protein sequences with peptide mass information from Rockefeller and NY Universities [or from Genomic Solutions]
  • ProteinProspector - UCSF tools for peptide masses data (MS-Fit, MS-Pattern, MS-Digest, etc.)
    • Identification and characterization with MS/MS data
      • Popitam ExPASy Proteomics tools - fhqdddddd - 流浪云南 - Identification and characterization tool for peptides with unexpected modifications (e.g. post-translational modifications or mutations) by tandem mass spectrometry
      • Phenyx ExPASy Proteomics tools - fhqdddddd - 流浪云南 - Protein and peptide identification/characterization from MS/MS data from GeneBio, Switzerland

      • Mascot - Sequence query and MS/MS ion search from Matrix Science Ltd., London
      • OMSSA - MS/MS peptide spectra identification by searching libraries of known protein sequences
      • PepFrag - Search known protein sequences with peptide fragment mass information from Rockefeller and NY Universities
      • ProteinProspector - UCSF tools for fragment-ion masses data (MS-Tag, MS-Seq, MS-Product, etc.)
      • xComb - computes all possible crosslinks based on proteins of interest for further interrogation using standard search engine ExPASy Proteomics tools - fhqdddddd - 流浪云南
      • xQuest - Search machine to identify cross-linked peptides from complex samples and large protein sequence databases ExPASy Proteomics tools - fhqdddddd - 流浪云南
      Identification with isoelectric point, molecular weight and/or amino acid composition
      • AACompIdent ExPASy Proteomics tools - fhqdddddd - 流浪云南 - Identify a protein by its amino acid composition
      • AACompSim ExPASy Proteomics tools - fhqdddddd - 流浪云南 - Compare the amino acid composition of a UniProtKB/Swiss-Prot entry with all other entries
      • TagIdent ExPASy Proteomics tools - fhqdddddd - 流浪云南 - Identify proteins with isoelectric point (pI), molecular weight (Mw) and sequence tag, or generate a list of proteins close to a given pI and Mw
      • MultiIdent ExPASy Proteomics tools - fhqdddddd - 流浪云南 - Identify proteins with isoelectric point (pI), molecular weight (Mw), amino acid composition, sequence tag and peptide mass fingerprinting data
      Other prediction or characterization tools
      • ProtParam ExPASy Proteomics tools - fhqdddddd - 流浪云南 - Physico-chemical parameters of a protein sequence (amino-acid and atomic compositions, isoelectric point, extinction coefficient, etc.)
      • Compute pI/Mw ExPASy Proteomics tools - fhqdddddd - 流浪云南 - Compute the theoretical isoelectric point (pI) and molecular weight (Mw) from a UniProt Knowledgebase entry or for a user sequence

      • GlycanMass ExPASy Proteomics tools - fhqdddddd - 流浪云南 - Calculate the mass of an oligosaccharide structure
      • PeptideCutter ExPASy Proteomics tools - fhqdddddd - 流浪云南 - Predicts potential protease and cleavage sites and sites cleaved by chemicals in a given protein sequence
      • PeptideMass ExPASy Proteomics tools - fhqdddddd - 流浪云南 - Calculate masses of peptides and their post-translational modifications for a UniProtKB/Swiss-Prot or UniProtKB/TrEMBL entry or for a user sequence

      • IsotopIdent ExPASy Proteomics tools - fhqdddddd - 流浪云南 - Predicts the theoretical isotopic distribution of a peptide, protein, polynucleotide or chemical compound
      HCD/CID spectra merger ExPASy Proteomics tools - fhqdddddd - 流浪云南 ExPASy Proteomics tools - fhqdddddd - 流浪云南 - a tool to merge the peptide sequence-ion m/z range from CID spectra and the reporter-ion m/z range from HCD spectra into the appropriate single file, to be further used in identification and quantification search engines
    • MALDIPepQuant ExPASy Proteomics tools - fhqdddddd - 流浪云南 - Quantify MALDI peptides (SILAC) from Phenyx output
    • MSight ExPASy Proteomics tools - fhqdddddd - 流浪云南 - Mass Spectrometry Imager
    • pIcarver ExPASy Proteomics tools - fhqdddddd - 流浪云南 - Visualize theoretical distributions of peptide pI on a given pH range and generate fractions with similar peptide frequencies
      • Other tools for 2-DE data (image analysis, data publishing, etc.)

        Translate ExPASy Proteomics tools - fhqdddddd - 流浪云南 - Translates a nucleotide sequence to a protein sequence
      • Transeq - Nucleotide to protein translation from the EMBOSS package
      • Graphical Codon Usage Analyser - Displays the codon bias in a graphical manner
      • BCM search launcher - Six frame translation of nucleotide sequence(s)

      • Reverse Translate - Translates a protein sequence back to a nucleotide sequence
      • (Reverse)-Transcription and Translation Tool

      • Genewise - Compares a protein sequence to a genomic DNA sequence, allowing for introns and frameshifting errors

        • BLAST ExPASy Proteomics tools - fhqdddddd - 流浪云南 Network Service on ExPASy
        • BLAST ExPASy Proteomics tools - fhqdddddd - 流浪云南 at EMBnet-CH/SIB (Switzerland)
        • BLAST at NCBI
        • WU-BLAST at Bork's group in EMBL (Heidelberg)
        • WU-BLAST and BLAST at the EBI (Hinxton)
        • BLAST at PBIL (Lyon)
            • Fasta3 - FASTA version 3 at the EBI
            • MPsrch - Smith/Waterman sequence comparison at EBI
            • PropSearch - Structural homolog search using a 'properties' approach at Montpellier
            • SAMBA - Systolic Accelerator for Molecular Biological Applications
            • SAWTED - Structure Assignment With Text Description
            • Scanps - Similarity searches using Barton's algorithm
            • SEQUEROME - BLAST similarity search and sequence profiling at Georgetown University
            • SHOPS - Analysis of the genomic operon context for any group of proteins

            • BLAST2FASTA - Converts NCBI BLAST output into FASTA format
          • InterPro Scan - Integrated search in PROSITE, Pfam, PRINTS and other family and domain databases
          • Hits ExPASy Proteomics tools - fhqdddddd - 流浪云南 - Relationships between protein sequences and motifs

          • ScanProsite ExPASy Proteomics tools - fhqdddddd - 流浪云南 - Scans a sequence against PROSITE or a pattern against the UniProt Knowledgebase (Swiss-Prot and TrEMBL)
          • HamapScan ExPASy Proteomics tools - fhqdddddd - 流浪云南 - Scans a sequence against the HAMAP families
          • MotifScan ExPASy Proteomics tools - fhqdddddd - 流浪云南 - Scans a sequence against protein profile databases (including PROSITE)
          • Pfam HMM search - Scans a sequence against the Pfam protein families db [At Washington University or at Sanger Centre]
          • ProDom - Compares sequences with ProDom search utility
          • SUPERFAMILY Sequence Search - Assign SCOP domains to your sequences using the SUPERFAMILY hidden Markov models
          • FingerPRINTScan - Scans a protein sequence against the PRINTS Protein Fingerprint Database
          • 3of5 - Complex Pattern Search - e.g. to search for a motif with 3 basic AA in 5 positions
          • ELM - Eukaryotic Linear Motif resource for functional sites in proteins
          • PRATT - Interactively generates conserved patterns from a series of unaligned proteins; [at EBI / ExPASy ExPASy Proteomics tools - fhqdddddd - 流浪云南]
          • PPSEARCH - Scans a sequence against PROSITE (allows a graphical output); at EBI
          • PROSITE scan - Scans a sequence against PROSITE (allows mismatches); at PBIL
          • PATTINPROT - Scans a protein sequence or a protein database for one or several pattern(s); at PBIL
          • SMART - Simple Modular Architecture Research Tool; at EMBL
          • TEIRESIAS - Generate patterns from a collection of unaligned protein or DNA sequences; at IBM

          • 9aaTAD - Prediction of Nine Amino Acid Transactivation Domain
            • ChloroP - Prediction of chloroplast transit peptides
            • LipoP - Prediction of lipoproteins and signal peptides in Gram negative bacteria
            • MITOPROT - Prediction of mitochondrial targeting sequences
            • PATS - Prediction of apicoplast targeted sequences
            • PlasMit - Prediction of mitochondrial transit peptides in Plasmodium falciparum
            • Predotar - Prediction of mitochondrial and plastid targeting sequences
            • PTS1 - Prediction of peroxisomal targeting signal 1 containing proteins
            • SignalP - Prediction of signal peptide cleavage sites

            • DictyOGlyc - Prediction of GlcNAc O-glycosylation sites in Dictyostelium
            • NetCGlyc - C-mannosylation sites in mammalian proteins
            • NetOGlyc - Prediction of O-GalNAc (mucin type) glycosylation sites in mammalian proteins
            • NetGlycate - Glycation of epsilon amino groups of lysines in mammalian proteins
            • NetNGlyc - Prediction of N-glycosylation sites in human proteins
            • OGPET - Prediction of O-GalNAc (mucin-type) glycosylation sites in eukaryotic (non-protozoan) proteins
            • YinOYang - O-beta-GlcNAc attachment sites in eukaryotic protein sequences

            • big-PI Predictor - GPI Modification Site Prediction
            • GPI-SOM - Identification of GPI-anchor signals by a Kohonen Self Organizing Map
            • Myristoylator ExPASy Proteomics tools - fhqdddddd - 流浪云南 - Prediction of N-terminal myristoylation by neural networks
            • NMT - Prediction of N-terminal N-myristoylation
            • CSS-Palm - Palmitoylation site prediction with CSS
            • PrePS - Prenylation Prediction Suite

            • NetAcet - Prediction of N-acetyltransferase A (NatA) substrates (in yeast and mammalian proteins)
            • NetPhos - Prediction of Ser, Thr and Tyr phosphorylation sites in eukaryotic proteins
            • NetPhosK - Kinase specific phosphorylation sites in eukaryotic proteins
            • NetPhosYeast - Serine and threonine phosphorylation sites in yeast proteins
            • GPS - Prediction of kinase-specific phosphorylation sites for 408 human protein kinases in hierarchy ExPASy Proteomics tools - fhqdddddd - 流浪云南
            • Sulfinator ExPASy Proteomics tools - fhqdddddd - 流浪云南 - Prediction of tyrosine sulfation sites
            • SulfoSite - Prediction of tyrosine sulfation sites
            • SUMOplot - Prediction of SUMO protein attachment sites
            • SUMOsp - Prediction of sumoylation sites
            • TermiNator - Prediction of N-terminal modification (version 3)

            • NetPicoRNA - Prediction of protease cleavage sites in picornaviral proteins
            • NetCorona - Coronavirus 3C-like proteinase cleavage sites in proteins
            • ProP - Arginine and lysine propeptide cleavage sites in eukaryotic protein sequences
              • NetNES Leucine-rich nuclear export signals (NES) in eukaryotic proteins
              • PSORT - Prediction of protein subcellular localization
              • SecretomeP - Non-classical and leaderless secretion of proteins
              • TargetP - Prediction of subcellular location
              • TatP - Twin-arginine signal peptides

              • DAS - Prediction of transmembrane regions in prokaryotes using the Dense Alignment Surface method (Stockholm University)
              • HMMTOP - Prediction of transmembrane helices and topology of proteins (Hungarian Academy of Sciences)
              • PredictProtein - Prediction of transmembrane helix location and topology (Columbia University)
              • SOSUI - Prediction of transmembrane regions (Nagoya University, Japan)
              • TMAP - Transmembrane detection based on multiple sequence alignment (Karolinska Institut; Sweden)
              • TMHMM - Prediction of transmembrane helices in proteins (CBS; Denmark)
              • TMpred ExPASy Proteomics tools - fhqdddddd - 流浪云南 - Prediction of transmembrane regions and protein orientation (EMBnet-CH)
              • TopPred - Topology prediction of membrane proteins (France)
                • ProtParam ExPASy Proteomics tools - fhqdddddd - 流浪云南 - Physico-chemical parameters of a protein sequence (amino-acid and atomic compositions, isoelectric point, extinction coefficient, etc.)
                • Compute pI/Mw ExPASy Proteomics tools - fhqdddddd - 流浪云南 - Compute the theoretical isoelectric point (pI) and molecular weight (Mw) from a UniProt Knowledgebase entry or for a user sequence
                • ScanSite pI/Mw - Compute the theoretical pI and Mw, and multiple phosphorylation states
                • MW, pI, Titration curve - Computes pI, composition and allows to see a titration curve
                • HeliQuest - A web server to screen sequences with specific alpha-helical properties

                • Radar - De novo repeat detection in protein sequences
                • REP - Searches a protein sequence for repeats
                • REPRO - De novo repeat detection in protein sequences
                • TRUST - De novo repeat detection in protein sequences
                • XSTREAM - De novo tandem repeat detection and architecture modeling in protein sequences

                • SAPS ExPASy Proteomics tools - fhqdddddd - 流浪云南 - Statistical analysis of protein sequences at EMBnet-CH [Also available at EBI]

                • Coils ExPASy Proteomics tools - fhqdddddd - 流浪云南 - Prediction of coiled coil regions in proteins (Lupas's method) at EMBnet-CH [Also available at PBIL]
                • Paircoil - Prediction of coiled coil regions in proteins (Berger's method)
                • Paircoil2 - Prediction of the parallel coiled coil fold from sequence using pairwise residue probabilitis with the Paircoil algorithm.
                • Multicoil - Prediction of two- and three-stranded coiled coils
                • 2ZIP - Prediction of Leucine Zippers

                • ePESTfind - Identification of PEST regions

                • HLA_Bind - Prediction of MHC type I (HLA) peptide binding
                • PEPVAC - Prediction of supertypic MHC binders
                • RANKPEP - Prediction of peptide MHC binding
                • SYFPEITHI - Prediction of MHC type I and II peptide binding

                • ProtScale ExPASy Proteomics tools - fhqdddddd - 流浪云南 - Amino acid scale representation (Hydrophobicity, other conformational parameters, etc.)
                • Drawhca - Draw an HCA (Hydrophobic Cluster Analysis) plot of a protein sequence
                • Peptide Builder
                • Protein Colourer - Tool for coloring your amino acid sequence
                • Three To One and One to Three - Tools to convert a three-letter coded amino acid sequence to single letter code and vice versa
                • Three-/one-letter amino acid converter - Tool which converts amino acid codes from three-letter to one-letter and vice versa.
                • Colorseq - Tool to highlight (in red) a selected set of residues in a protein sequence
                • HelixWheel / HelixDraw - Representations of a protein fragment as a helical wheel

                • RandSeq ExPASy Proteomics tools - fhqdddddd - 流浪云南 - Random protein sequence generator
                  • AGADIR - An algorithm to predict the helical content of peptides
                  • APSSP - Advanced Protein Secondary Structure Prediction Server
                  • GOR - Garnier et al, 1996
                  • HNN - Hierarchical Neural Network method (Guermeur, 1997)
                  • HTMSRAP - Helical TransMembrane Segment Rotational Angle Prediction
                  • Jpred - A consensus method for protein secondary structure prediction at University of Dundee
                  • JUFO - Protein secondary structure prediction from sequence (neural network)
                  • NetSurfP - Protein Surface Accessibility and Secondary Structure Predictions ExPASy Proteomics tools - fhqdddddd - 流浪云南
                  • nnPredict - University of California at San Francisco (UCSF)
                  • Porter - University College Dublin
                  • PredictProtein - PHDsec, PHDacc, PHDhtm, PHDtopology, PHDthreader, MaxHom, EvalSec from Columbia University
                  • Prof - Cascaded Multiple Classifiers for Secondary Structure Prediction
                  • PSA - BioMolecular Engineering Research Center (BMERC) / Boston
                  • PSIpred - Various protein structure prediction methods at Brunel University
                  • SOPMA - Geourjon and Deléage, 1995
                  • SSpro - Secondary structure prediction using bidirectional recurrent neural networks at University of California
                  • DLP-SVM - Domain linker prediction using SVM at Tokyo University of Agriculture and Technology
                    • iMolTalk - An Interactive Protein Structure Analysis Server
                    • MolTalk - A computational environment for structural bioinformatics
                    • COPS - Navigation through fold space and the instantaneous visualization of pairwise structure similarities
                    • PoPMuSiC - Prediction of thermodynamic stability changes upon point mutations; design of modified proteinsExPASy Proteomics tools - fhqdddddd - 流浪云南
                    • Seq2Struct - A web resource for the identification of sequence-structure links
                    • STRAP - A structural alignment program for proteins
                    • TLSMD - TLS (Translation/Libration/Screw) Motion Determination
                    • TopMatch-web - Protein structure comparison
                      • Tertiary structure prediction
                        Homology modeling
                        • SWISS-MODEL ExPASy Proteomics tools - fhqdddddd - 流浪云南 - An automated knowledge-based protein modelling server
                        • 3Djigsaw - Three-dimensional models for proteins based on homologues of known structure
                        • CPHmodels - Automated neural-network based protein modelling server
                        • ESyPred3D - Automated homology modeling program using neural networks
                        • Geno3d - Automatic modelling of protein three-dimensional structure
                        • SDSC1 - Protein Structure Homology Modeling Server
                        Threading
                        • Phyre (Successor of 3D-PSSM) - Automated 3D model building using profile-profile matching and secondary structure
                        • Fugue - Sequence-structure homology recognition
                        • HHpred - Protein homology detection and structure prediction by HMM-HMM comparison
                        • Libellula - Neural network approach to evaluate fold recognition results
                        • LOOPP - Sequence to sequence, sequence to structure, and structure to structure alignment
                        • SAM-T02 - HMM-based Protein Structure Prediction
                        • Threader - Protein fold recognition

                        • SWEET - Constructing 3D models of saccharides from their sequences
                        Ab initio
                        Assessing tertiary structure prediction
                        • Anolea - Atomic Non-Local Environment Assessment
                        • LiveBench - Continuous Benchmarking of Structure Prediction Servers
                        • NQ-Flipper - Validation and correction of asparagine and glutamine side-chain amide rotamers in protein structures solved by X-ray crystallography
                        • PROCHECK - Verification of the stereochemical quality of a protein structure
                        • ProSA-web - Recognition of errors in 3D structures of proteins
                        • QMEAN ExPASy Proteomics tools - fhqdddddd - 流浪云南 - Server for Model Quality Estimation
                        • What If - Protein structure analysis program for mutant prediction, structure verification, molecular graphics
                        Quaternary structure
                        • MakeMultimer - Reconstruction of multimeric molecules present in crystals

                        • EBI PISA - Protein Interfaces, Surfaces and Assemblies
                        • PQS - Protein Quaternary Structure Query form at the EBI
                        • ProtBud - Comparison of asymmetric units and biological units from PDB and PQS
                        Molecular modeling and visualization tools
                        Prediction of disordered regions

                        SIM + LALNVIEW ExPASy Proteomics tools - fhqdddddd - 流浪云南 - Alignment of two protein sequences with SIM, results can be viewed with LALNVIEW
                      • LALIGN ExPASy Proteomics tools - fhqdddddd - 流浪云南 - Finds multiple matching subsegments in two sequences
                      • Dotlet ExPASy Proteomics tools - fhqdddddd - 流浪云南 - A Java applet for sequence comparisons using the dot matrix method
                        • Multiple
                          Alignment analysis
                          • AMAS - Analyse Multiply Aligned Sequences
                          • Bork's alignment tools - Various tools to enhance the results of multiple alignments (including consensus building).
                          • CINEMA - Color Interactive Editor for multiple alignments
                          • ESPript - Tool to print a multiple alignment
                          • MaxAlign - Post-processing of alignments by removing sequences (taxa) with many gaps
                          • PhyloGibbs ExPASy Proteomics tools - fhqdddddd - 流浪云南 - Gibbs motif sampler incorporating phylogeny and tracking statistics
                          • SVA - Sequence Variability Analyser for multiple alignments
                          • PVS - A protein variability server optimized for conserved epitope discovery

                          • WebLogo - Sequence logos at Berkeley/USA
                          • plogo - Sequence logos at CBS/Denmark
                          • GENIO/logo - Sequence logos at Stuttgart/Germany
                          • SeqLogo - Sequence logos at the Immunomedicine Group, Facultad de Medicina, U.C.M, Spain (The Molecular Immunology Foundation (MIF) does not exist anymore)

                          BIONJ - Server for NJ phylogenetic analysis
                        • DendroUPGMA
                        • PHYLIP - Server for phylogenetic analysis using the PHYLIP package
                        • PhyML - Server for ML phylogenetic analysis
                        • Phylogeny.fr - Robust Phylogenetic Analysis For The Non-Specialist
                        • The PhylOgenetic Web Repeater (POWER) - Performs phylogenetic analysis

                        • BlastO - Blast on orthologous groups
                        • Evolutionary Trace Server (TraceSuite II) - Maps evolutionary traces to structures

                        • Phylogenetic programs - List of phylogenetic packages and free servers (PHYLIP pages)
                          • AcroMed - A computer generated database of biomedical acronyms and the associated long forms extracted from the recent Medline abstracts
                          • BioMinT - Mining the biomedical literature
                          • GPSDB - Gene and Protein Synonym DataBase
                          • Medline RankerExPASy Proteomics tools - fhqdddddd - 流浪云南
                          • The Miner Suite - of bioinformatic software packages and data analysis
                          • XplorMed - Explore a set of abstracts derived from a bibliographic search in MEDLINE
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