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 Home : Products : Kodon : Features & modules
Modules and Features of the Kodon Software
Kodon offers the following main features:

  • Fully integrated analysis platform, from raw sequencer chromatograms to megabase sequences, with full back-tracking functionality.
  • GenBank and EMBL are Kodon’s native formats. No conversion, no loss of features and qualifiers from documented sequences.
  • Project-oriented multi-user database environment; unlimited capacity. Choice between local, file-based databases and server-based Oracle, PostgreSQL, Microsoft SQL Server, Access, and other database engines. Possibility to connect to existing databases.
  • Storage and full analysis capability on local computers. No need to upload data over the Internet, avoiding network traffic, enhancing data security, and ensuring faster return of results.
  • Automatic updates of databases from public servers.
  • Advanced structured queries of any complexity for searches in local or external databases.
  • Rich and uniform sequence annotation display in all analysis tools: vector cloning, ligation, primer design, alignment, homology search, match and repeat analysis, ...
  • Feature matrix to search and select related features out of chromosome sequences and analyze them by multiple alignment and clustering.
  • Chromosome dot plot matrix to visualize homologous regions in and between chromosomes. Automatic search for repeats and duplicates to locate paralogous and orthologous genes.
  • In-silico cloning and restriction analysis with unparalleled functions and rich, publication-ready output possibilities. Simulation of agarose gels with restriction fragment patterns and size markers.
  • Primer design on sequences, chromosomes, and multiple alignments of DNA or protein sequences. Temperature and degeneration plots, search for distinctive primers for PCR detection, and many other features.
  • Prediction of RNA and protein secondary structure, helical wheel analysis, motif search, prediction of Leucine zippers, and physico-chemical property analysis.
  • The finest multiple alignment editor that exists, offering a wealth of alignment, clustering and phylogenetic inference functions.
  • Computationally intensive tasks such as multi-chromosome mapping run in background threads and can be interrupted and resumed whenever desired.
  • Script language for automation of tasks, import & export, generation of custom reports, personalization of interface, etc.

Kodon consists of a Basic Software and three modules for specific applications. The main functionality of the modules is as follows:

  • Kodon Basic Software: contig assembly, database and advanced querying, sequence editor, restriction enzyme analysis, homology search (BLAST)
  • Multiple Alignment, Clustering and Phylogeny: sequence selection from feature matrix, multiple Alignment, clustering and phylogeny (UPGMA, Neighbor Joining, Parsimony, Maximum Likelihood)
  • Molecular Analysis: vector construction, primer design, frame analysis, RNA and protein secondary structure, pairwise matching and repeat analysis, motif search and physico-chemical properties analysis
  • Chromosome Mapping: side-by-side comparison of genomes and chromosomes, analysis of organization and functional behaviour of genomes, chromosome annotation

The full Kodon functionality is physically contained in the same program unit, which guarantees perfect integration of the modules, a consistent user interface, and no tedious switching between programs.

Network Licenses of Kodon
 Compatibility

© 2008 Applied Maths NV