Downloadable & Online Tools
On-line tools and databases
The research projects performed by groups in the Center involve the construction of new software tools. Invention of new approaches or computational procedures are accompanied by development of software tools and testing them on the problem data. Tools that prove useful are made available to the biomedical research world as downloadable tools/databases, or as online services.
List of on-line tools and databases:
|
Group |
Tool name |
Purpose |
|---|---|---|
|
Ben-Tal / Pupko/ Mayrose |
Identify functional regions in proteins |
|
|
Wolfson |
Rigid unbound docking of molecules |
|
|
Mayrose |
The chromosome counts database |
|
|
Mayrose |
Analysis of genotype clustering results |
|
|
Pupko |
Confidence scoring of elements in alignment |
|
|
Ben-Tal/ Pupko |
Identify functional regions in proteins |
|
|
Wolfson |
Refine protein-protein docking solutions |
|
|
Pupko |
Ancestral sequence reconstruction |
|
|
Pupko |
Identify site-specific selection |
|
|
Pupko |
Epitope mapping using affinity-selected peptides |
|
|
Ast |
Identification of all splice signals |
|
|
Ast |
Analysis of splice signals |
|
|
Shomron |
miRNA regulation of drug metabolism |
|
|
Pupko |
Analyze 0/1 matrices in an evolutionary context |
|
|
Pupko |
Co-evolution of presence-absence patterns |
|
|
Shamir |
Revealing missing genes in biological pathways |
|
|
Ben-Tal/ Pupko |
Identification of functional regions in proteins |
|
|
Ben-Tal |
Suggest alternative protein conformations |
|
|
Ben-Tal/ Pupko/ Mayrose |
Identify functionally & structurally important residues in proteins |
|
|
Pupko |
Confidence score in multiple sequence alignment |
|
|
Ast |
Identify exonic splicing regulator sequences |
|
|
Gat-Viks |
DCQ (Digital Cell Quantifier) combines genome Digital cell quantifier |
|
|
Pupko/Mayrose |
Detect trait-dependent shifts in the rate of sequence evolution |
|
|
Shamir |
Expression and mutation-based analysis for many diseases |
|
|
Pupko |
Detect immunogenic regions in proteins |
|
|
Wolfson |
Functional Sites Structural Search Engine |
|
|
Shomron |
Mapping population of viral genomes |
|
|
Wolfson |
Refinement and binding-affinity estimation of peptide inhibitors |
|
|
Wolfson |
Flexible refinement of docking solutions |
|
|
Wolfson |
Pharmacophore detection |
|
|
Wolfson |
Peptide-inhibitor ant colony design algorithm |
|
|
Ben-Tal |
Protein mutant stability analyzer |
|
|
Wolfson |
Complementarity docking of rigid protein and flexible DNA shape |
|
|
Wolfson |
Simultaneous alignment of multiple protein structures |
|
|
Wolfson |
Membrane protein docking algorithm |
|
|
Wolfson |
Structural modeling of multi-molecular protein complexes |
|
|
Ast |
Identify the branch site sequence |
|
|
Pupko |
Bayesian simulator of DNA sequences |
|
|
Ben-Tal |
Effect of mutations on protein's function |
|
|
Gat-Viks |
Identify alterations in cell quantities discriminating between disease states |
|
|
Ast |
Identify microRNA located within transposons |
|
|
Ast |
Transposable elements in protein-coding genes |
|
| Borenstein | BURRITO | Interactive visualization of taxonomic and functional microbiome data |
| Pupko | ASAP | Immunoglobulin-sequencing analysis pipeline |
| Pupko | M1CR0B1AL1Z3R | Analyze large-scale bacterial genomics data |
| Pupko | PASA | Proteomics Analysis of Serum Antibodies |
