Pedant-Pro™ Sequence Analysis Suite

The Pedant-Pro™ Sequence Analysis Suite is a genome analysis package for fast, comprehensive, enterprise-scale 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.

Biomax offers high-quality, comprehensive analysis of entire genomes including automatic and manual annotation using the Pedant-Pro Sequence Analysis Suite.

"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

Read more

Click for full-sized image and more screen shots

Benefits for researchers

  • Process large amounts of sequences with multi-method analysis in minimum time
  • Create and maintain your organization's central sequence, target and protein repository
  • Produce comparable results over numerous analyses
  • Integrate and analyze high-throughput single nucleotide polymorphism (SNP) data
  • Simplify strain improvement using genome and pathway comparison
  • Easily find potential diagnostic and drug targets matching required properties
  • 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)
  • Add your own data: manually annotate gene functions, modify gene predictions, include experimental data and integrate proprietary databases

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
Selected references

PEDANT covers all complete RefSeq genomes.
Walter MC, Volz A, Pongratz N, Jost R, Mewes HW, Frishman D, et al.
Nucleic Acids Res 37: (Database issue) D408-11 (2009) Abstract Full text

PEDANT genome database: 10 years online.
Riley L, Schmidt T, Wagner C, Volz A, Artamonova I, Heumann K, Mewes HW, Frishman D
Nucl Acids Res 35: (Database issue) D354-7 (2007) Abstract Full text

The PEDANT genome database in 2005: 334 genomes on the Web.
Riley L, Schmidt T, Wagner C, Mewes HW, Frishman D
Nucl Acids Res 33: D308-10 (2005) Abstract Full text

The PEDANT genome database.
Frishman D, Mokrejs M, Kosykh D, Kastenmueller G, Kolesov G, et al.
Nucl Acids Res 31: 207-11 (2003) Abstract Full text

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

PEDANTic genome analysis.
Frishman D and Mewes HW Trends in Genetics 13: 415-6 (1997)