[ 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.