We present the first exact method based on the topology of a metabolic network to find minimal sets of metabolites (called precursors) sufficient to produce a set of target metabolites. In contrast with previous proposals, our model takes into account self-regenerating metabolites involved in cycles, which may be used to generate target metabolites from potential precursors. We analyse the complexity of the problem and we propose an algorithm to enumerate all minimal precursor sets for a set of target metabolites. The algorithm can be applied to identify a minimal medium necessary for a cell to ensure some metabolic functions. It can be used also to check inconsistencies caused by misannotations in a metabolic network. We present two illustrations of these applications. © 2008 Springer-Verlag Berlin Heidelberg.
Enumerating precursor sets of target metabolites in a metabolic network / Cottret, Ludovic; Paulo Vieira, Milreu; Vicente, Acuna; MARCHETTI SPACCAMELA, Alberto; Fabio Viduani, Martinez; Marie France, Sagot; Stougie, Leen. - STAMPA. - 5251 LNBI:(2008), pp. 233-244. (Intervento presentato al convegno 8th International Workshop on Algorithms in Bioinformatics, WABI 2008 tenutosi a Karlsruhe nel 15 September 2008 through 19 September 2008) [10.1007/978-3-540-87361-7_20].
Enumerating precursor sets of target metabolites in a metabolic network
MARCHETTI SPACCAMELA, Alberto;
2008
Abstract
We present the first exact method based on the topology of a metabolic network to find minimal sets of metabolites (called precursors) sufficient to produce a set of target metabolites. In contrast with previous proposals, our model takes into account self-regenerating metabolites involved in cycles, which may be used to generate target metabolites from potential precursors. We analyse the complexity of the problem and we propose an algorithm to enumerate all minimal precursor sets for a set of target metabolites. The algorithm can be applied to identify a minimal medium necessary for a cell to ensure some metabolic functions. It can be used also to check inconsistencies caused by misannotations in a metabolic network. We present two illustrations of these applications. © 2008 Springer-Verlag Berlin Heidelberg.File | Dimensione | Formato | |
---|---|---|---|
VE_2008_11573-215180.pdf
solo gestori archivio
Tipologia:
Versione editoriale (versione pubblicata con il layout dell'editore)
Licenza:
Tutti i diritti riservati (All rights reserved)
Dimensione
235.45 kB
Formato
Adobe PDF
|
235.45 kB | Adobe PDF | Contatta l'autore |
I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.