MrBac: a web server for draft metabolic network reconstructions for bacteria.
Genome-scale metabolic network reconstruction can be used for simulating cellular behaviors by simultaneously monitoring thousands of biochemical reactions, and is therefore important for systems biology studies in microbes. However, the labor-intensive and time-consuming reconstruction process has hindered the progress of this important field. Here we present a web server, MrBac (Metabolic network Reconstructions for Bacteria), to streamline the network reconstruction process for draft genome-scale metabolic networks and to provide annotation information from multiple databases for further curation of the draft reconstructions. MrBac integrates comparative genomics, retrieval of genome annotations, and generation of standard systems biology file format ready for network analyses. We also used MrBac to automatically generate a draft metabolic model of Salmonella enteric serovar Typhimurium LT2. The high similarity between this automatic model and the experimentally validated models further supports the usefulness and accuracy of MrBac. The high efficiency and accuracy of MrBac may accelerate the advances of systems biology studies on microbiology. MrBac is freely available at http://sb.nhri.org.tw/MrBac.
Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan 350, Taiwan.
Yu-Chieh
YC
Liao
Julie Chih-Yu
JC
Chen
Min-Hsin
MH
Tsai
Yueh-Hsia
YH
Tang
Feng-Chi
FC
Chen
Chao A
CA
Hsiung
D019295:Computational Biology / Q000379:methods; D003198:Computer Simulation; D016680:Genome, Bacterial; D023281:Genomics / Q000295:instrumentation* / Q000379:methods; D020407:Internet / Q000295:instrumentation*; D053858:Metabolic Networks and Pathways; D012486:Salmonella typhimurium / Q000235:genetics / Q000378:metabolism*; D012984:Software