Tools and Software

Prediction of membrane proteins

• • PRED-TMBB2: Improved topology prediction and detection of beta-barrel outer membrane proteins 

  • HMMpTM: Combined prediction of membrane protein topology and post-translational modification 

  • ConBBPRED: Consensus Prediction of TransMembrane Beta-Barrel Proteins

  • PRED-TMBB:Predicting and discriminating beta-barrel outer membrane proteins with Hidden Markov Models

  • HMM-TM: A Hidden Markov Model method for the topology prediction of alpha-helical membrane proteins that incorporates experimentally derived topological information (Mirror at the University of Athens)

  • MCMBB: Discrimination of beta-barrel outer membrane proteins with a Markov chain model

  • PRED-COUPLE 2: A tool that predicts the coupling specificity of G-protein coupled receptors to G-proteins

  • PRED-COUPLE: A method that implements refined profile Hidden Markov Models to predict the coupling specificity of G-protein coupled receptors to G-proteins

  • PRED-GPCR: GPCR Family Classification from sequence alone based on a probabilistic method that uses family-specific profile Hidden Markov Models

Prediction of Signal peptides

• • PRED-TAT: Prediction of twin-arginine signal peptides

  • PRED-SIGNAL: Prediction of signal peptides in archaea (Mirror at the University of Athens). 

  • PRED-LIPO: Prediction of Lipoprotein Signal Peptides in Gram-positive Bacteria with a Hidden Markov Model (Mirror at the University of Athens).  

  • CW-PRED: Prediction of Cell Wall-Anchored Proteins in Gram-positive Bacteria

  • CW-PREDv2:  Prediction of C-terminal surface anchoring sorting signals in bacteria and Archaea (NEW)

  • PredSL: Prediction of Subcellular Location from the N-terminal Sequence

Sequence analysis

• • migma: The Mixture Transition Distribution model for biological sequence analysis 

  • NON-RED:  A web tool to select biological sequences from a given set, with similarity/homology less than a user-defined level

  • vizHMM:  A tool for visual representation of Hidden Markov Models

  • JUCHMME: Biological sequence analysis using Class Hidden Markov Models (CHMM) 

Biological Network analysis

• powerClust is an easy-to-use web application for clustering analysis and visualization of bipartite graphs

Databases

• • OMPdb: a database of beta-barrel outer membrane proteins from Gram-negative bacteria

  • ExTopoDB: A database of experimentally derived topological models of transmembrane proteins 

  • human_gpDB: A database of human GPCRs, G-proteins, Effectors and their interactions 

  • gpDB:  a database of G-proteins and their interaction with GPCRs

Biostatistics Software

• metagen: STATA program for meta-analysis of genetic association studies

• metatrend: STATA program for estimating trends in cumulative meta-analysis

• STATA programs for multivariate meta-analysis of genetic association studies including models for continuous and discrete outcomes, prospective and retrospective likelihood, and the genetic model-free approach

• Poisson meta-analysis: Mixed-Effects Poisson Regression Models for Meta-Analysis of Follow-Up Studies with Constant or Varying Durations 

• Haplotype meta-analysis: STATA programs for meta-analysis of haplotype association studies 

• meta-tdt: Meta-analysis of Family-based and Case-control Genetic Association Studies That Use the Same Cases 

• Robust meta-analysis: robust methods for analysis and meta-analysis of GAS and GWAS

• meta-ROC: meta-analysis for comparison of diagnostic tests 

• gllamm: meta-analysis in STATA using gllamm 

• regression: the covariance of regression coefficients calculated from summary data 

• multiple: A Multivariate Method for Meta-Analysis of Multiple Outcomes in Genetic Association Studies 

• GWAR: Tools for Robust Analysis and Meta-Analysis of Genome-Wide Association Studies 

• PRED-LD: An efficient tool for GWAS summary statistics Imputation (NEW)