B I O T E C H N O L O G Y

BIOTECHNOLOGY: Excerpt of User List

• Applied Biosystems
• Celera Genomics
• GlaxoSmithKline
• Hoffmann LaRoche
• InfoSys
• Max Planck Institute for Molecular Genetics
• Max-Planck Institute for Biochemistry
• TIGR

EXAMPLE OF USE: Celera

Celera Genomics used LEDA to decode the Human Genome – Celera used LEDA during the assembly phase of the project by applying sophisticated techniques in order to sequence the fragments of the genome into their proper order. LEDA continues to provide both suitable data structures and algorithms as well as the visualization of substructures of the DNA, thus allowing interactive modification of the resulting subsequences. For this, fast and exact computational methods - as implemented in LEDA - are crucial, especially for processing large amounts of data.

FEATURE: Graph Isomorphisms and Subgraph Isomorphisms

Molecular structures can easily be modeled as graphs. An important question is whether a given structure contains specific substructures. In graph theory, this problem is answering the question whether two graphs are isomorphic to each other. With its powerful graph data type and its related types and algorithms, LEDA provides all ingredients necessary to solve such problems.
Gabriel Valiente has proven in 'Algorithms on Trees and Graphs ', Springer Verlag Berlin, 2002, that algorithms computing graph isomorphy can easily be built upon LEDA. Starting LEDA version 5.1 LEDA provides its own collection of graph isomorphism algorithms, a module with state-of-the-art implementations for the testing of graph and subgraph isomorphisms.

With the new module LEDA graph isomorphisms you receive efficient algorithms for your subgraph testing problems. Read the paper Graph Isomorphism Implementation in LEDA 5.1 for more details, have a look in the 5.1 manual and play around with the demo program demo/graph_iso/gw_isomorphism.cpp (part of your LEDA package).

VISUALIZATION: Visualization of Structures  

LEDA easily supports the abstract modeling of biological structures. Such models can be visualized in a clear and informative way.

See for LEDA: GraphWin

Specials:

• Organic Layout, e.g., for Biochemical Reaction Networks