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Figure 2 | BMC Genomics

Figure 2

From: Structured RNAs and synteny regions in the pig genome

Figure 2

Homology based annotation in overview. The Venn diagrams for counting the high confident structured RNA loci found with sequence homology search (BLAST), structure homology search (Infernal) and class specific tools (tRNAscan-SE, snoStrip, and RNAmmer). (a) The diagram includes all 3,418 high confident structured RNA loci obtained by homology. (b) The similarity search is confined to the Rfam seed sequences (excluding the miRNA families in Rfam). 19 loci found by high confident BLAST against the Rfam sequences is missed by high confident structure homology search (18 + 1 in the red and purple areas of the right hand side of the figure). The reason is our additional Infernal E-value cutoff of 1e-3 imposed on all families. See text for detailed discussion. The numbers in parenthesis are after removal of 12 tRNAs and 15 miRNAs loci removed in the cleanup procedure. A total of 3,391 RNA loci were found. Of these 1,011 loci were found by sequence similarity, 2,314 were found by structure similarity, and 1,505 were detected by class specific methods.

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