FLIM-MAP: Gene Context Based Identification of Functional Modules in Bacterial Metabolic Pathways

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 co...

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Bibliographic Details
Published in:Frontiers in microbiology 2018-09, Vol.9, p.2183-2183
Main Authors: Bhatt, Vineet, Mohapatra, Anwesha, Anand, Swadha, Kuntal, Bhusan K, Mande, Sharmila S
Format: Article
Language:English
Subjects:
annotation
bacteria
functional potential
gene context
genome
metabolic pathway
Microbiology
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Summary: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.
ISSN:1664-302X
1664-302X
DOI:10.3389/fmicb.2018.02183