Pedant-Pro™ Sequence Analysis Suite

The Pedant-Pro™ Sequence Analysis Suite is a genome analysis package for comprehensive analysis of DNA and protein sequences. The software annotates individual sequences and entire genomes automatically, provides an easy-to-use interface for exploring genomic data and allows users to manually refine data for additional detail. The Pedant-Pro databases constitute a powerful and concise sequence, gene and protein repository — an ideal foundation for efficient research and development (R&D) processes. Cross-genome comparison (including positional linkage and phylogenetic profiling) extends the Pedant-Pro suite with tools for work in the industrial biotechnology sector.

"The Pedant-Pro genome analysis of the filamentous fungus Aspergillus niger provided quickly a high-quality automatic annotation of the enzyme pool and was the ideal basis for a detailed manual annotation. This enabled our R&D department to identify the required proteases and bring an improved product to the market in reasonable time. For this and for other projects, Pedant-Pro has proven to be indispensable in our development pipeline."

— Herman Pel, Principal Scientist Genomics and Bioinformatics at DSM

Pedant-Pro genome analysis is used to help sport drink market breakthrough

In September 2004, DSM launched its specialist sports recovery drink, PeptoPro Sports with its core ingredient PeptoPro. These active peptides increase the rate of muscle recovery considerably and won the Gold Award for innovation in health ingredients at the industry-leading Hi Europe exhibition.

The use of proteins in ready-to-use sports drinks was limited up to then because of bitter taste and bad solubility.

To find a solution for addressing this issue, DSM performed the complete analysis and annotation of the Aspergillus niger genome with the aid of the Pedant-Pro Sequence Analysis Suite. This revealed several new proteases, which were subsequently patented. The proprietary mix of enzymes is now used to digest casein and to provide a high quality source of small, quickly absorbable peptides with excellent taste, PeptoPro.

References:

Pel HJ et al (2007) Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88. Nat Biotechnol 25:221-31

http://www.dsm.com/en_US/html/dfs/peptopro_home.htm

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Benefits for researchers

  • Process large amounts of sequences with multi-method analysis in minimum time
  • Produce comparable results over numerous analyses
  • Simplify strain improvement using genome and pathway comparison
  • Find easily potential diagnostic and drug targets matching required properties
  • Add your own data: manually annotate gene functions, modify gene predictions, include experimental data and integrate proprietary databases
  • Visualize gene and protein properties using an easy-to-use graphical interface
  • Take advantage of expert knowledge and experience: use an optimized multi-method system without evaluating and managing the individual bioinformatic algorithms
  • Process entire method sets or subsets according to current requirements (e.g., perform exhaustive genome analysis or design your own workflow with protein domain analysis only)

Benefits for companies

  • Enable optimal adaptation to the requirements of unique R&D processes through a dynamic workflow architecture: use standard workflows defined by Biomax scientists or specially design workflows for your projects
  • Save time and money in the sequence analysis process: use the high-throughput, industrial-scale Pedant-Pro grid-processing engine to analyze a maximum number of genomes, ESTs or other sequences in a minimum of time
  • Use the highly efficient EST pre-processing pipeline, streamlining the EST analysis process
  • Work with exactly the genomes you need: have your company or project-specific cross-genome comparison data set generated as a perfect basis for microbial analyses in industrial biotechnology.
  • Create a company-wide gene index with manual annotation functionalities for distributed systems, allowing all scientists of a project to access the active genomes easily
  • Save training time and money by providing an easy-to-use graphical user interface which allows efficient work for the bioinformatician as well as for the laboratory biologist from the first minute on

The Pedant-Pro Sequence Analysis Suite has been used at Biomax to annotate over 450 genomes in the PEDANT Genome Database.

Selected Reference

Functional and structural genomics using PEDANT.
Frishman D, Albermann K, Hani J, Heumann K, Metanomski A, Zollner A, Mewes HW.
Bioinformatics 17(1):44-57(2001) Abstract