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For this analysis, the number of sequences with significant identity to each metabolic gene in a functional category in the SEED subsystem database were normalised to the sequencing effort for each sample (Fig. 1) and sequences which could not be annotated in this way were not included.
These form a useful resource for benchmarking, but since a rather small fraction of functional sites are likely to be annotated in this database, the benchmark here uses synthetic sequence that contains embedded REDfly footprints as well as synthetic samples from PWMs, as described in Materials and Methods.
The GC-skew graph (Figure 1) shows a significant inversion upstream of the dnaA and 6 putative dnaA boxes were located near the same gene, providing additional evidence that the origin of replication can be annotated in this region of the genome.
Approximately 29% (77,591/263,425) of the cowpea GSRs could be annotated in this way.
It is possible that a larger percentage could not be annotated in this study due to technical limitations, such as sequencing depth or read length [ 30], that are common to all studies that perform de novo transcriptome analyses.
Once all output identifiers had been annotated in this manner, we calculated a score based on the number of input identifiers (In), the number of input identifiers for which at least one output identifier was returned (Hits), the total number of returned output identifiers (Out), and the number of preferred output identifiers (Matches).
Three porcine pseudo-genes and four novel genes were annotated in this region.
Seven genes had been annotated in this segment of D. mojavensis chromosome 2 and we designed primers to amplify the intergenic region between each pair of genes in this species, as well as in D. buzzatii strains with and without inversion 2z3.
However, only about 18,000 3′-UTRs annotatedated in this version.
Finally, a total of 30,601unigenes were annotated in this manner.
