DEF: an automated dead-end filling approach based on quasi-endosymbiosis

• DOI: 10.1093/bioinformatics/btw604
• Publication Date: 2016-09-27T02:35:45Z
• Authors: Lili Liu; Zijun Zhang; Taotao Sheng; Ming Chen
• Keywords: Endosymbiosis; Dead end; End-to-end principle

Gap filling for the reconstruction of metabolic networks is to restore connectivity metabolites via finding high-confidence reactions that could be missed in target organism. Current methods gap either fall into network topology or have limited capability missing are indirectly related dead-end but biological importance model.We present an automated (DEF) approach, which derived from wisdom endosymbiosis theory, fill gaps by most efficient utilization paths a constructed quasi-endosymbiosis model. The recalls and dead ends DEF reach around 73% 86%, respectively. This method capable dead-end-related with organism applicable any given In E. coli iJR904 model, instance, about 42% were fixed our proposed method.DEF publicly available at http://bis.zju.edu.cn/DEF/[e-mail] data Bioinformatics online.