Tools and Software

Here you will find the computational biology tools developed by members of our group. The older tools are hosted at the web-server of the Department of Cell Biology and Biophysics of the University of Athens. You can also download some STATA programs for meta-analysis developed by us.


Prediction of membrane proteins

  • PRED-TMBB2: Improved topology prediction and detection of beta-barrel outer membrane proteins (NEW)
  • HMMpTM: Combined prediction of membrane protein topology and post-translational modification (NEW)
  • 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

Sequence analysis

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

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 (NEW)
  • gllamm: meta-analysis in STATA using gllamm (NEW)
  • regression: the covariance of regression coefficients calculated from summary data (NEW)
  • multiple: A Multivariate Method for Meta-Analysis of Multiple Outcomes in Genetic Association Studies (NEW)
  • GWAR: Tools for Robust Analysis and Meta-Analysis of Genome-Wide Association Studies (NEW)