Finding metabolic pathways using atom tracking.
BACKGROUND
Finding novel or non-standard metabolic pathways, possibly spanning multiple species, has important applications in fields such as metabolic engineering, metabolic network analysis and metabolic network reconstruction. Traditionally, this has been a manual process, but the large volume of metabolic data now available has created a need for computational tools to automatically identify biologically relevant pathways.


RESULTS
We present new algorithms for finding metabolic pathways, given a desired start and target compound, that conserve a given number of atoms by tracking the movement of atoms through metabolic networks containing thousands of compounds and reactions. First, we describe an algorithm that identifies linear pathways. We then present a new algorithm for finding branched metabolic pathways. Comparisons to known metabolic pathways demonstrate that atom tracking enables our algorithms to avoid many unrealistic connections, often found in previous approaches, and return biologically meaningful pathways. Our results also demonstrate the potential of the algorithms to find novel or non-standard pathways that may span multiple organisms.


BACKGROUND
The software is freely available for academic use at: http://www.kavrakilab.org/atommetanet.


BACKGROUND
Supplementary data are available at Bioinformatics online.
Heath
Allison P
AP
Department of Computer Science, Rice University, Houston, TX, USA.
Bennett
George N
GN
Kavraki
Lydia E
LE
D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D053858:Metabolic Networks and Pathways