Mapping genomic features to functional traits through microbial whole genome sequences Online publication date: Fri, 24-Oct-2014
by Wei Zhang; Erliang Zeng; Dan Liu; Stuart E. Jones; Scott Emrich
International Journal of Bioinformatics Research and Applications (IJBRA), Vol. 10, No. 4/5, 2014
Abstract: Recently, the utility of trait-based approaches for microbial communities has been identified. Increasing availability of whole genome sequences provide the opportunity to explore the genetic foundations of a variety of functional traits. We proposed a machine learning framework to quantitatively link the genomic features with functional traits. Genes from bacteria genomes belonging to different functional traits were grouped to Cluster of Orthologs (COGs), and were used as features. Then, TF-IDF technique from the text mining domain was applied to transform the data to accommodate the abundance and importance of each COG. After TF-IDF processing, COGs were ranked using feature selection methods to identify their relevance to the functional trait of interest. Extensive experimental results demonstrated that functional trait related genes can be detected using our method. Further, the method has the potential to provide novel biological insights.
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