Sentence examples for metabolic reconstructions using from inspiring English sources
This result makes possible the estimation of time scales associated with other available metabolic reconstructions, using their metabolome data and without necessarily requiring a complete knowledge of kinetic parameters.
Beyond experimental evidence, it is possible to assess the likelihood of reactions in genome-scale metabolic reconstructions using theoretical models.
Both systems also have tools for metabolic reconstruction using KEGG (Kyoto encyclopedia of genes and genomes) for sequence comparisons using BLAST and for functional comparisons using KEGG or FIGfam.
The metabolic reconstruction used here [ 3] lacks such a sink for metabolism.
Draft metabolic reconstructions generated using homology-based comparisons unavoidably contain some omissions and misclassifications.
Finally, to detect sources, we applied the Borenstein's method [ 75] on the two metabolic reconstructions independently, using the Igraph package (R software) [ 76].
Automated protein function prediction was then performed using a number of databases including protein domains (Pfam) [88], UniProt [89], TIGRFAMs [90], KEGG [59], Interpro [91], and COG [20]; metabolic reconstruction analysis using PRIAM [58]; signal peptide prediction using SignalP [39]; tRNA prediction using tRNAscan-SE [92]; and rRNA prediction using RNAmmer [93].
Additional file 1: FASTCORMICS allows fast context-specific metabolic model reconstruction using microarray data.
Genome-scale metabolic reconstructions are used extensively in the study of microbial metabolism and have proven powerful tools to guide rational pathway design of industrial strains.
The catabolism of cellulose hydrolysis products by F. succinogenes was characterized further by performing a metabolic reconstruction analysis using the software program PRIAM [58] to generate KEGG pathway maps [59].
Constraint-based analysis using genome-scale metabolic reconstructions is a widely used computational tool for predicting how fluxes through microbial metabolic pathways will respond to changes in the culture environment or gene deletions/insertions [ 26, 27].
