Flim-Map: gene context based identification of functional modules in bacterial metabolic pathways

Title Flim-Map: gene context based identification of functional modules in bacterial metabolic pathways
Publication TypeJournal Article
Year of Publication2018
AuthorsBhatt, V, Mohapatra, A, Anand, S, Kuntal, BK, Mande, SS
JournalFrontiers in microbiology
Volume9
Date PublishedSEP
Type of ArticleArticle
Abstract

Prediction of functional potential of bacteria can only be ascertained by the accurate annotation of its metabolic pathways. Homology based methods decipher metabolic gene content but ignore the fact that homologs of same protein can function in different pathways. Therefore, mere presence of all constituent genes in an organism is not sufficient to indicate a pathway. Contextual occurrence of genes belonging to a pathway on the bacterial genome can hence be exploited for an accurate estimation of functional potential of a bacterium. In this communication, we present a novel annotation resource to accurately identify pathway presence by using gene context. Our tool FLIM-MAP (Functionally Important Modules in bacterial Metabolic Pathways) predicts biologically relevant functional units called 'GCMs' (Gene Context based Modules) from a given metabolic reaction network. We benchmark the accuracy of our tool on amino acids and carbohydrate metabolism pathways.

DOI10.3389/fmicb.2018.02183
Type of Journal (Indian or Foreign)

Foreign

Impact Factor (IF)

4.019

Divison category: 
Chemical Engineering & Process Development