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Gene and protein analysis programs and databases on line  

2010-12-12 19:46:06|  分类: 生物信息分析 |  标签: |举报 |字号 订阅

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Gene and protein analysis programs and databases

Gene information retrieval Integrated DNA/Protein Analysis Start sites Sequence Analysis
Sequence alignment servers Sequence comparison servers Sequence submission servers Protein Motif and Modification Prediction Servers
Modified Protein Databases Protein Secondary Structure Prediction Servers Threading Fold Databases

Gene information retrieval

Integrated DNA/Protein Analysis

Start sites

Sequence Analysis

Sequence alignment servers

  • BLOCK Maker (protein homology blocks)
  • CLUSTALW
  • CLUSTALW and CLUSTALX - Download
  • CINEMA - Viewer for aligned sequences
  • AMAS - Analyse Multiply Aligned Sequences
  • MEME & MAST (motif search and alignment)
  • Match-Box - multiple protein sequence alignment based on strict statistical criteria.
  • MUSCLE - Multiple sequence comparison by log-expectation.
  • PipeAlign PipeAlign is an on-line protein family analysis tool providing both interactive and automatic workbench for the validation, integration and presentation of the biological insights resulting from the analysis.
  • PRALINE - multiple sequence alignment with many options (e.g. global or local preprocessing, predicted secondary structure information and iteration capabilities) to optimise the information for each of the input sequences.

Sequence comparison servers

Sequence submission servers

Protein Subcellular Location, Motif, and Modification Prediction Servers

    Prediction of Protein Subcellular Location 

  • ChloroP - Prediction of N-terminal chloroplast transit peptide, and, if predicted, the probable site for cleavage of the transit peptide.
  • Golgi Predictor - Prediction of Golgi Type II membrane proteins based on their transmembrane domains
  • Locate - A Protein Subcellular Localization Database
  • LocSVMpsi - protein subcellular LOCalization based on SVM and PSI-blast v.1.3
  • MITOPROT - Prediction of mitochondrial targeting sequences
  • PredictNLS - an automated tool for the analysis and determination of Nuclear Localization Signals (NLS).
  • Predotar - Prediction of mitochondrial and plastid targeting sequences
  • PTS1 - Prediction of peroxisomal targeting signal 1 containing proteins
  • SecretomeP - The SecretomeP 1.0b server produces ab initio predictions of non-classical i.e. not signal peptide triggered protein secretion in eukaryotes.
  • SignalP Server - Predictions of the presence and location of signal peptide cleavage sites in amino acid sequences from prokaryotes and eukaryotes.
  • TargetP - TargetP predicts the subcellular location of eukaryotic protein sequences and the potential cleavage site for sequences predicted to contain a chloroplast transit peptide (cTP), mitochondrial targeting peptide (mTP) or secretory pathway signal peptide (SP).

    General Protein Motif Resources

  • DeltaMass - A Database of Protein Post Translational Modifications
  • ELM - Eukaryotic linear motif resource for functional sites in proteins
  • Prosite - Database of protein families and domains including functional patterns
  • Resid - comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications.
  • QuasiMotiFinder - A server for the identification of signatures and signature-like patterns in protein sequences
  • ScanMot - searching for similar sequences using a simultaneous scan of multiple sequence motifs.

    Specialized Protein Motif Resources

  • Big-PI predictor - GPI modification site prediction.
  • CANSITE - Scan your protein for potential signaling effector and adaptor sites
  • DictyOGlyc 1.1 Server - Predictions of GlcNAc O-glycosylation sites in Dictyostelium discoideum proteins.
  • GPI-SOM - Identification of GPI-anchor signals by a Kohonen Self Organizing Map
  • GPS - Group-based phosphorylation scoring method
  • KinasePhos - Prediction of protein phosphorylation sites.
  • Myristoylator - Prediction of N-terminal myristoylation by neural networks
  • NetAcet - Prediction of N-acetyltransferase A (NatA) substrates (in yeast and mammalian proteins)
  • NetOGlyc 2.0 Server - Predictions of mucin type GalNAc O-glycosylation sites in human proteins.
  • NetNES - neural network predicts leucine-rich nuclear export signals (NES) in eukaryotic proteins using a combination of neural networks and hidden Markov models.
  • NetNGlyc 1.0 Server - Predictions of N-glycosylation sites in mammalian proteins.
  • NetPhos - neural network predictions for serine, threonine and tyrosine phosphorylation sites in eukaryotic proteins.
  • NetPhosK - neural network predictions of kinase specific eukaryotic protein phosphorylation sites.
  • NMT - The MYR predictor - Predicts N-terminal N-Myristoylation of Proteins.
  • PhosphoELM - A database of phosphorylation sites with a phosphorylation prediction program.
  • Sulfinator - Predicts tyrosine sulfation sites in protein sequences.
  • SUMOplot - Prediction of SUMO protein attachment sites
  • SIFT - Predictions of amino acid substitutions on protein function
  • YinOYang - neural network predictions for O-beta-GlcNAc attachment sites in eukaryotic protein sequences.

Modified Protein Databases

Protein Interactions

  • Biomolecular InteractioN Database - full descriptions of interactions, molecular complexes and pathways.
  • DIP - Database of Interacting Proteins.
  • HPID - Human Protein Interaction Database
  • MINT - Molecular INTeraction database.
  • OPHID - The Online Predicted Human Interaction Database.
  • PRISM - PRotein Interactions by Structural Matching (v 0.93)
     

Protein Secondary Structure Prediction Servers

(partly from:  http://vl.bwh.harvard.edu/proteins.shtml )
 

Threading

Fold Databases

Homology Modelling

Molecule Graphics

ref: http://www.humgen.nl/programs.html

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