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Figure 1 | BMC Genomics

Figure 1

From: A systematic search for new mammalian noncoding RNAs indicates little conserved intergenic transcription

Figure 1

Summary of computational prediction and sorting of novel mammalian noncoding RNA. (a) Whole genome alignments were downloaded from UCSC [18], subset to regions of greater than 85% sequence identity, and analyzed with QRNA [14]. Removal of redundant and coding sequences left 36,756 ncRNA candidates containing 62 known ncRNAs (of approximately 400 known ncRNAs). Candidates were then sorted and the top 3,478 predicted RNAs, which contained 38 known ncRNAs (representing a 1,700 fold enrichment of real ncRNAs over random selection from genomic sequence), were selected for further screening. (b) Sorting was based on the QRNA score, stability (measured as a predicted free energy change using Mfold [44]), overlap with rat-mouse QRNA predictions, and genomic clustering (many predictions close to one another are likely the same transcript). This combination of four criteria was more powerful in identifying real ncRNAs than using the QRNA score alone. *UCSC [18], **See (b).

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