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Servers
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
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
Microarrays
- Base a comprehensive free web-based database solution
- Base in Uppsala
- Baseplugins produced at LCB
Misc
- 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
Programs
- 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,
Databases
- 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
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
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
Microarrays
- Base a comprehensive free web-based database solution
- Base in Uppsala
- Baseplugins produced at LCB
Misc
- 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
Programs
- 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,
Databases
- 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