Fig. 2

Comparison between the length difference of candidates from 6frame search and the NCBI annotation of E. coli, expressed as fraction of the total protein length. A value of \(0\%\) (red dotted line) indicates that candidate and annotation are identical. Negative values mean that the candidate is shorter than the annotated protein due to lack of coverage by PSMs towards the N-terminus. Positive values imply that the candidate has a longer N-terminal sequence than that indicated in the annotation. Below, the N-terminus of the fatty acyl-CoA synthetase FadD is shown in the UCSC Genome Browser. The first track shows the reading frame of the genome on the negative strand. The second track shows the current annotation. After this the gene annotation is shown as predicted by RNAcode [8]. The next line shows a bar plot representation of the mapped reads per base of the transcriptomic data. At the bottom track the mapped PSMs are depicted. It is misannotated and extends to canonical start. Our extension of this reading-frame is supported by evidence of conserved coding sequences determined by RNAcode