Bioinformatics, Algorithmics and Data Mining Group

Public web services

These are the bioinformatics tools and databases developed in the BIIT research group in Tartu, Estonia. Most of the tools have public free web access interfaces. For others we are currently developing such interfaces. More tools and databases are on the way... Interested? Please contact and give feedback.

Tutorials and Training on BIIT software tools

Databases and integrated atlases

• MEM - Multi-Experiment-Matrix -- large-scale gene expression data queries and mining (Genome Biology 2009)
• FunGenES consortium data atlas - mouse embryonic stem cell development and differentiation database (PLoS One 2009)
• Embryonic stem cells database (ESCDb)  (PLoS One 2010)

Web tools

• g:Profiler family of tools for functional assessment of gene groups, gene ID mappings, orthology and expression similarity searches. (NAR web server issue 2007)
  
  • g:Profiler - g:Gost - functional profiling of gene lists
  • g:Gost - functional profiling of ranked (or sorted) gene lists 
  • g:Cocoa - comparative functional profiling
    
  • g:Convert - batch manipulations and conversions of gene id-s and names between different database IDs
  • g:Orth - batch mapping of gene id-s to their orthologs
  • g:Sorter - querying gene expression data for similar gene profiles (see MEM for multi-data-set queries)
• m:explorer - identifying process-specific gene regulators from high-throughput genomic data (Genome Biology 2012)
• KEGGanim - animation of pathways using high-throughput data (Bioinformatics 2007/2008)
• GraphWeb - a tool for mining large biological networks (graphs)(NAR Web Server Issue 2008)
• VisHiC - visualisation of hierarchical clustering based on functional annotations (NAR Web Server Issue 2009)
  
• G=MAT: Linking Transcription Factor Expression with DNA Binding(under review)
• URLMAP - Web tool and databases integration over simple web GUI.
• BIIT Link -. a replacement of tinyurl like service, supports also POST methods!

Algorithms and other software and resources

• HappieClust - Fast Approximate Hierarchical Clustering (BioData Mining 2009)
• SPEXS pattern discovery algorithm and tool for DNA and protein analysis(Vilo 1997; 1998, 2000, 2001, 2002)
• BiGeR - a database and tools of gene regulation information

• SWOG - Simpe Web Object Graphics, a web graphics programming language based on perl&GD or Java.
• Medical informatics data handling and analysis: software for databasing case report forms (CRF), biomedical metadata, etc. (See publication and product description) 

  Quretec Data Management Platform.

• Information retrieval related algorithms and data structures
  • Search of Russian words in latin alphabet (Estonian); old Estonian words; etc based on universal edit distance engine
  • Search of English words based on pronunciation (in Estonian)
  • Very fast approximate regular expression matching using shift-OR based automaton matching

Older software

• Expression Profiler tools (@EBI)
  and new Expression Profiler: Next Generation (collaboration with the EBI)
  Note - since EBI discontinued the maintenance of Expression Profiler, please let me know who would be interested to use tha version? We will install it at our BIIT servers then. Please contact Jaak Vilo.
• Pattern discovery methods
  • G-Protein Coupled receptor (GPCR) coupling specificity predictions

Main contact: Prof. Jaak Vilo