JCVI Prokaryotic Annotation Pipeline

The automated Prokaryotic Annotation Pipeline was developed to generate on demand ORF prediction and functional annotation for prokaryotic genomes. A round of non-coding RNA prediction is done using various tools such as tRNA-scanSE and BLAST. Gene finding is done using a self-training, iterated glimmer3 analysis. The predicted genes are then analyzed for overlaps, and homology based evidence is gathered using a system of hidden markov model search and BLAST. Roles and gene symbols are assigned to the predictions based on the above analyses, common names, GO terms, and EC numbers. The genes are also translated and run through transcript level computes, including a COG analysis, motif finding, and peptide signal identification. The pipeline produces a functionally annotated genome, including RNAs and various genome characteristics, creating a stepping stone for further analysis.