Swedish bioinformatics services available online

A list of bioinformatic tools developed partly or fully by bioinformaticians in Sweden. If you miss a tool, please contact mikael.borg@bils.se.

Tool About Owner
ACID A database server for information about reporters/probes/genes used in microarray experiments Lund university
BARC A a freely available catalogue describing expertise and molecular analysis resources available at centers and companies in Sweden for analysis of biobanked samples. Uppsala university
ChemGPS-NP A tool tuned for navigation in biologically relevant chemical space Uppsala University
Chlamydia trachomatis MLST Chlamydia trachomatis multilocus sequence typing (MLST) database Uppsala University
ChloroP Prediction of chloroplast transit peptides Stockholm Bioinformatics Centre
CYP11B1 CYP11B1 mutation browser Linköping university
CYP21 CYP21 mutation browser Linköping university
DAS Prediction of Transmembrane Regions Stockholm Bioinformatics Centre
ΔG prediction Prediction of apparent free energy difference for a potential transmembrane helix Center for Biomembrane Research
DRIP-PRED Disorder/order prediction for proteins Stockholm Bioinformatics Centre
EGMRG Encyclopedia of microbiota regulated genes Gothenburg university
EVALLER A web-tool wherein you can electronically test a proteins potential allergenicity/cross-reactivity based on its amino acid sequence Livsmedelsverket (National food administration)
FISH - profile search Family Identification with Structure Anchored Hidden Markov Models Umeå university
FISH - sequence search Family Identification with Structure Anchored Hidden Markov Models Umeå university
FragHMMent Residue-residue contact prediction Linköping university
FunCoup Global networks of functional coupling in eukaryotes from comprehensive data integration Stockholm Bioinformatics Centre
The Human Protein Atlas Database with millions of high-resolution images Uppsala University, KTH
GPCRHMM A hidden Markov model for GPCR detection Stockholm Bioinformatics Centre
Inparanoid A database of orthologs in eukaryotes Stockholm Bioinformatics Centre
Kalign Fast and accurate multiple alignments Stockholm Bioinformatics Centre
MDR database Medium-chain dehydrogenases/reductases database Linköping university
MolMeth A structured database that provides best practice-based protocols for molecular analyses Uppsala university
MultiDisp A tool for analysing and visualising multiple sequence alignments (MSAs) Lund university
Normalyzer Quantitative data set overview and normalization Lund University
NucPred Nuclear localization prediction Stockholm Bioinformatics Centre
OAT Ontology annotation treebrowser Linköping university
OCTOPUS Prediction of membrane protein topology and signal peptides Center for Biomembrane Research
OnD-CRF Predicting Order and Disorder in proteins using Conditional Random Fields Umeå university
Orthodisease A database of disease gene orthologs Stockholm Bioinformatics Centre
p53 p53 mutation browser Linköping university
Pcons Protein structure prediction meta server Stockholm Bioinformatics Centre
Pfam A database of protein domain families Stockholm Bioinformatics Centre
Phobius A combined transmembrane topology and signal peptide predictor Stockholm Bioinformatics Centre
Pmembr A threading method for membrane proteins Stockholm Bioinformatics Centre
PON-Diso A method to predict changes in disorder regions contained in protein caused by amino acid substitutions. Lund university
PON-P2 Predicts the pathogenicity of amino acid substitutions. Lund university
PPSC Prediction of Protein Stability Changes. Lund university
PrIMETV Visualize tree reconciliations Stockholm Bioinformatics Centre
PROPHECY Profiling of phenotypic characteristics in Yeast Gothenburg university
ProQ A protein model quality predictor Stockholm Bioinformatics Centre
RSpred A Rifin/Stevor prediction tool Karolinska Institutet, Linköping university
RetroTector A rational tool for analysis of retroviral elements in small and medium size vertebrate genomic sequences Uppsala university
SCAMPI Prediction of membrane protein topology from first principles Center for Biomembrane Research
SDRDB Short-chain dehydrogenases/reductases database Karolinska Institutet, Linköping university
SFINX Multiple predictions of functional and structural features in proteins in an integrated graphical environment Stockholm Bioinformatics Centre
SignalP Prediction of signal peptides Stockholm Bioinformatics Centre
SPECLUST A web-based application to cluster lists of peptide peak masses, typically extracted from protein mass spectra Lund university
SVMHC Prediction of MHC class I binding peptides Stockholm Bioinformatics Centre
SwePep An endogenous peptide database Uppsala University
TargetP Prediction of protein subcellular localisation Stockholm Bioinformatics Centre
TMHMMfix Topology prediction of membrane proteins with optional fixing and reliability score calculation Stockholm Bioinformatics Centre
TOPCONS Consensus prediction of membrane protein topology Center for Biomembrane Research
UniCarb-DB A database of LC-MS structural data for oligosaccharides Gothenburg university

Swedish bioinformatics services available for download

Tool About Owner
Autophylo An automatic pipeline for phylogenetic analysis Uppsala University
BASE A comprehensive free web-based database solution for the massive amounts of data generated by microarray analysis Lund university
Belvu Calculate trees from multiple alignments Stockholm Bioinformatics Centre
Bioclipse Free and open source workbench for the life sciences Uppsala University
Dasher A Java DAS client for displaying annotations on a protein sequence Stockholm Bioinformatics Centre
Dotter A dot-matrix program with interactive greyscale rendering for genomic DNA and Protein sequence analysis Stockholm Bioinformatics Centre
jSquid A java tool to visualize networks and edge scores Stockholm Bioinformatics Centre
LEPRA Protein modeling program Stockholm Bioinformatics Centre
LGscore To measure quality of a protein model Stockholm Bioinformatics Centre
MesoRD A tool for stochastic simulation of reactions and diffusion. Uppsala University
modhmm A modular HMM program used in PRO(DIV)-TMHMM and other studies Stockholm Bioinformatics Centre
MrBayes Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. NRM
Palign An alignment/threading program Stockholm Bioinformatics Centre
Patchwork A bioinformatic tool for analyzing and visualizing allele-specific copy numbers and loss-of-heterozygosity in cancer genomes. Uppsala University
PQPQ Matlab code and test data for protein quantification by peptide quality control. Science for Life Laboratory
Proteios Software Environment A multi-user platform for analysis and management of proteomics data Lund university
ssHMM Secondary structure HMMs based on HMMER Stockholm Bioinformatics Centre