Figure 4.

Data used for determination of ncRNA candidates in Streptococcus pyogenes. This screenshot shows an example of the data used to find intergenic regions that may contain ncRNA genes. The first row contains annotations from the Genbank file downloaded from NCBI. Green and blue bars correspond to protein genes. The second row contains the hand-picked candidate regions. The blue block delimits the region where an ncRNA is suspected. Start and end of this region are not accurate as the methods used do not allow for exact determination of the transcript. The red lines indicate the start and end of the candidate regions for visual orientation. The third row contains the RNAfold minimum free energy profile, a clear peak is visible indicating a strong RNA structure. Row four contains the DNA base stacking energy profile, two peaks delimit the candidate region and a third peak is inside, from our visual inspection of all intergenic regions this profile is notably different. Row five and six contain the scores for each window of the analysed genome for a BLAST search against all Streptococcus genomes and against all Streptococcus pyogenes genomes respectively, notable are the conserved regions outside the protein genes. The last row contains the RNAz predictions. The shades of blue in lines 2-7 correspond to the height of the respective bars. Screenshots for all four candidates are given on the moses website.

Raasch et al. BMC Bioinformatics 2010 11:491   doi:10.1186/1471-2105-11-491
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