Figure 3.

Screenshot of a pipeline created with the Graphical User Interface. A simple genome annotation pipeline is shown, consisting of four gene prediction analyses (GlimmerHMM, Genscan, GeneID and SNAP), an intron-exon splice-site prediction (GeneSplicer), a tRNA gene predictor (tRNAscan-SE), a MAR element scan (Marscan), a repeat analysis (Tandem Repeat Finder) and a BLASTX analysis. The predicted genes (stored as coordinates on the original sequence; GFFCds) are converted into a sequence object (GenericTranscriptSequence) and subsequently subjected to a BLASTX analysis against the NCBI NT database.