BIOINFORMATICS DEVELOPMENT
Since 2003 we develop software for biologists
We implement bioinformatics project in various directions.These are new algorithms; optimization af legal interfaces and algorithms; development of computational pipelines; integration of different methods, applications and databases. Cloud, cluster and special processors computations are available on demand. We can implement custom solutions on basis of UGENE platform as well as development new projects from scratch. Also possible is reengineering of existing customer’ software.
Open source cross-platform toolkit Unipro UGENE for complex genome analysis integrates various popular algorithms and methods, renders highly interactive GUI.
Features:
- Analysis, annotations, search of structural elements
- NGS data processing, genome variations search
- Sequence alignment and phylogeny
- Cloning, In silico PCR
- Access to remote databases
- Workflow Designer for pipeline data processing
- Support multiple biological data formats
- Automation of small labs via shared database
- Easy adoption of external tools
- HPC options for many algorithms
Technologies:
C++, Qt toolkit, JQuery, Java, JIRA, TeamCity
GeneCut software is designed for in silico experiments in gene assembly (already in action) and molecular cloning (under development). Computing results obtained serve as the basis for subsequent laboratory experiments. The key features are as follows:
- Reverse translation of amino acid sequence.
- Codon optimization for an input nucleotide sequence.
- Removal of specific sites from a nucleotide sequence.
- Splitting of nucleotide sequence into oligonucleotides for subsequent assembly using one of two methods: PCA or TBIO.
- Partitioning of nucleotide sequence into long blocks for subsequent assembly using one of two methods: Gibson assembly or Overlap extension PCR.
- Cloning of one or several fragments into a plasmid using one of two methods: Gibson assembly or Gateway. This feature is currently under development.
Technologies:
C++, Qt toolkit, GitLab
Customer, one of the leaders in biotechnology domestic market within synthesis of oligonucleotides and test systems for RT-PCR, it also produces equipment for molecular analysis. The company requested the improvement of the software for the genetic analyzer. The project was successfully implemented and became part of the firmware of a serially produced device. This made it possible to combine device-generated data with widely used international formats and process them more efficiently.
Technologies:
C++, QT toolkit, Java
Software for processing and analysis of large amount of SNP genomic variations. Powerful integrated database, comprised of refined data from mostly known world molecular biological data sources. Graphical interface and stream data processing substantialy lighten user efforts. Beta-version is on testing stage.
Features:
- database with all known genes, SNPs and their annotations, relation to deseases, damaging effect matrices
- high-capacity set of filters
- selection of candidate variations with large damaging effect
- fast processing of big data arrays
- multi-tier visualization and firendly user interface
- vast options for customization
- multi-platform support
Technologies:
C++, Qt toolkit, JIRA, JQuery, Java
Our bionformatics team developed 3 specific algorithms for processing libraries of 16sRNA gene of microbial communities on UGENE platform basis.
Technologies:
C++, Qt toolkit
Web-application on Windows Azure cloud, enabling in details to monitor status of all run tasks, workload of computational capacities and users authorization.
Technologies:
C++, Qt toolkit, Java, MS Azure