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[ Jump to Programs and Databases ]

Services

* Services that are marked with * are not hosted at SBC but were developed fully or partly by people at SBC.

Phylogeny

  • PRIMETV: Visualize tree reconciliations
  • Belvu: Calculate trees from multiple alignments.

Protein structure analysis

  • * Pcons Consensus fold recognition and meta server with homology modelling..
  • Pmembr A threading method for membrane proteins.
  • * 3D-PSSM A fold recognition server
  • ProQ A protein model quality predictor.

Transmembrane predictions

  • Phobius A combined transmembrane topology and signal peptide predictor.
  • * ZPRED Predicting the distance to the membrane center for residues in alpha-helical membrane proteins.
  • PRODIV-TMHMM Topology and reentrant predictions.
  • TMHMMfix TMHMM with optional fixing and reliability score calculation.
  • * TopPred A TM predictor that uses the positive inside rule
  • DAS Prediction of Transmembrane Regions.

Protein localisation prediction

  • NucPred Nuclear localization prediction.
  • * TargetP Prediction of protein subcellular localisation
  • * SignalP Prediction of signal peptides
  • * ChloroP Prediction of chloroplast transit peptides

Sequence analysis tools

  • Dasher: A Java DAS client for displaying annotations on a protein sequence.
  • SFINX: Multiple predictions of functional and structural features in proteins in an integrated graphical environment.
  • GPCRHMM: A hidden Markov model for GPCR detection
  • Kalign: Fast and accurate multiple alignments
  • DRIP-PRED Disorder/order prediction for proteins.
  • GPCPRED Contact map prediction for proteins.
  • SVMHC Prediction of MHC class I binding peptides.
  • PhylProM Phylogenetic profiles
  • OVOP automatic view generation for protein structures (source code available)
  • * NetOGlyc Prediction of mucin-type O-glycosylation
  • * NetCGlyc Prediction of C-mannosylation

Program packages

  • Dotter: A dot-matrix program with interactive greyscale rendering for genomic DNA and Protein sequence analysis
  • modhmm A modular HMM programed used in PRO(DIV)-TMHMM and other studies..
  • LGscore A program to measure the similarity between proteins.
  • Palign Our alignment/threading programs.
  • ssHMM Secondary structure HMMs based on HMMER
  • LEPRA Protein modelling C++ /library.
  • Gromacs A fast molecular dynamics program
  • Modelestimator: Estimate protein replacement rates
  • LAPD: Estimate evolutionary distance from protein alignments
  • Biblio: Interact with PubMed on the command line
  • jSquid: A java tool to visualize networks and edge scores.

Databases

  • FunCoup: Global networks of functional coupling in eukaryotes from comprehensive data integration.
  • Pfam: A database of protein domain families. Pfam is a large collection of multiple sequence alignments and hidden Markov models covering many common protein domains.
  • Inparanoid: A database of orthologs in eukaryotes. InParanoid is a program that automatically detects orthologs (or groups of orthologs) from 2 species. This WWW page presents an interface for browsing orthologs detected by InParanoid.
  • Orthodisease: A database of disease gene orthologs.
  • UniDomInt: A comprehensive database of domain-domain interactions.
  • MultiParanoid: A multi-species version of InParanoid.

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