TY - JOUR
T1 - FindPath
T2 - a Matlab solution for in silico design of synthetic metabolic pathways
AU - Vieira, Gilles
AU - Carnicer, Marc
AU - Portais, Jean Charles
AU - Heux, Stéphanie
N1 - Publisher Copyright:
© The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: [email protected].
PY - 2014/10/15
Y1 - 2014/10/15
N2 - SUMMARY: Several methods and computational tools have been developed to design novel metabolic pathways. A major challenge is evaluating the metabolic efficiency of the designed pathways in the host organism. Here we present FindPath, a unified system to predict and rank possible pathways according to their metabolic efficiency in the cellular system. This tool uses a chemical reaction database to generate possible metabolic pathways and exploits constraint-based models (CBMs) to identify the most efficient synthetic pathway to achieve the desired metabolic function in a given host microorganism. FindPath can be used with common tools for CBM manipulation and uses the standard SBML format for both input and output files.AVAILABILITY AND IMPLEMENTATION: http://metasys.insa-toulouse.fr/software/findpath/.CONTACT: [email protected] INFORMATION: Supplementary data are available at Bioinformatics online.
AB - SUMMARY: Several methods and computational tools have been developed to design novel metabolic pathways. A major challenge is evaluating the metabolic efficiency of the designed pathways in the host organism. Here we present FindPath, a unified system to predict and rank possible pathways according to their metabolic efficiency in the cellular system. This tool uses a chemical reaction database to generate possible metabolic pathways and exploits constraint-based models (CBMs) to identify the most efficient synthetic pathway to achieve the desired metabolic function in a given host microorganism. FindPath can be used with common tools for CBM manipulation and uses the standard SBML format for both input and output files.AVAILABILITY AND IMPLEMENTATION: http://metasys.insa-toulouse.fr/software/findpath/.CONTACT: [email protected] INFORMATION: Supplementary data are available at Bioinformatics online.
UR - http://www.scopus.com/inward/record.url?scp=84921803508&partnerID=8YFLogxK
UR - https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=pure_univeritat_ramon_llull&SrcAuth=WosAPI&KeyUT=WOS:000343083600026&DestLinkType=FullRecord&DestApp=WOS_CPL
U2 - 10.1093/bioinformatics/btu422
DO - 10.1093/bioinformatics/btu422
M3 - Article
C2 - 24994891
AN - SCOPUS:84921803508
SN - 1367-4811
VL - 30
SP - 2986
EP - 2988
JO - Bioinformatics (Oxford, England)
JF - Bioinformatics (Oxford, England)
IS - 20
ER -