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How to carry out functional annotation of bacterial transcriptomic data?

Experimental question Created on 11 Jun 2014

Details

I am currently using KEGG and UNIPROT to manually assign functional annotations to the expression data obtained from Staphylococcus lugdunensis transcriptome (RNAseq). Does anyone have any tips or knows any tools for (automated) GO enrichment analysis with bacterial expression data? 

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