Bioinformatics in Sweden

Research Groups
Conferences & Meetings
Teaching & Courses
Links to Grants etc
  To be updated, if you want to add something please contact: Arne Elofsson


Homology search and fold recognition

  • Pfam A database of protein domain families.
  • 3D-PSSM A fold recognition server
  • Pcomb Fold recognition server.
  • Pcons The first consensus fold recognition.
  • Pmembr A threading method for membrane proteins.

Membrane protein and protein localization

  • TopPred A TM predictor that uses the positive inside rule
  • tmHMM An older HMM method to predict transmembrane regions.
  • TMAP A TM predictor that uses multiple sequence alignments
  • PRO-TMHMM A profile based version of TMHMM.
  • PRODIV-TMHMM The currently best method to predict transmembrane regions.
  • DAS Prediction of Transmembrane Regions.

Protein localization

  • ChloroP Prediction of chloroplast transit peptides
  • SignalP Prediction of signal peptides
  • TargetP Prediction of protein subcellular localisation
  • PeroxiP Prediction of peroxisomal proteins
  • Phobius A combined transmembrane topology and signal peptide predictor

Protein Structure

  • ProQ A protein model quality predictor.
  • OVOP automatic view generation for protein structures

Evolutionary and gene function related

  • Orthostrapper Extracts orthology support values from trees.
  • Inparanoid A database of orthologs in eukaryotes.
  • Orthodisease A database of disease gene orthologs.
  • HOPS Hierarchical grouping of Orthologous and Paralagous sequences.
  • PhylProM Phylogenetic profiles



  • AOpredict A server to predict effective Antisense Oligonucleotides.
  • AOsearch Check your Antisense Oligonucleotides for Specificity
  • OligoControlDesigner Design controls for your Antisense Oligonucleotide
  • siSearch Design siRNA molecules using standard design rules
  • Chromowheel ChromeWheel is a processing method for generating interactive illustrations of genome data.
  • SVMHC Prediction of MHC class I binding peptides.
  • PubGene Gene co-citation neighbors


  • SFINX Prediction of functional and structural features in proteins.
  • Belvu Belvu is an X-windows viewer for multiple sequence alignments.
  • Dotter A dot-matrix program with interactive greyscale rendering for genomic DNA and Protein sequence analysis
  • MSP Crunch A filtering tool for Blast matches
  • Stockholm The "Stockholm" format is a system for marking up features in a multiple alignment.
  • modhmm A modular HMM programed used in PRO(DIV)-TMHMM and other studies..
  • LEPRA Protein modelling C++ /library.
  • LGscore A program to measure the similarity between proteins.
  • Palign An alignment/threading program.
  • ssHMM Secondary structure HMMs based on HMMER
  • Sfixem A java version of Blixem
  • Blixem an interactive browser of pairwise Blast matches
  • Gromacs A fast molecular dynamics program
  • Base a comprehensive free web-based database solution
  • eGOn A tool for mapping microarray data onto the Gene Ontology structure
  • JExpress Gene expression data analysis
  • ROSETTA a toolkit for analyzing tabular data within the framework of rough set theory.
  • Spectronet A package for the analysis and visualization of complex evolutionary data
  • VisRD A Java program that implements exploratory visual approaches,


  • KIND A nonredundant database.
  • TAED The Adaptive Evolution Database.
  • Pfam A database of protein domain families.

Locations for lists of Servers and Databases

  • Stockholm Bioinformatics Center
    • Fold Recognition
    • Structural Bioinformatics Tools
    • Transmembrane Topology prediction
    • Protein Localisations
    • Databases
  • Sonnhammer Group at CGB, KI
    • Ortholog Detection and Analysis
    • Protein Function / Transmembrane Topology / Structure Analysis
    • Protein Domain Family Analysis
    • Antisense Oligonucleotide and siRNA Design Tools
    • Other Analysis Tools

Arne Elofsson
Last modified: Fri Mar 24 16:35:23 CET 2006