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Figure 1 | BMC Genomics

Figure 1

From: Structured RNAs and synteny regions in the pig genome

Figure 1

Pipeline. The modules of the RNA pipeline. Module 1 (annotation): The annotation pipeline takes as input any number of sequences and runs a number of external annotation tools on it (see text for details). This leads to the initial annotation of the RNA loci in the sequence. A naming and resolving tool decides on the final annotation of the locus. The 3,393 ncRNA genes cover 11 conflicts of annotation, 34 loci moved to the medium confident annotation during the curation step, 165 novel miRNA loci found exclusively by miRDeep, and 3,183 ncRNA genes found by homology. LncRNA loci and cis-regulatory elements are annotated separately. Module 2 (multiple alignments): The multiple alignment pipeline runs on a genomic scale and aligns the genomic sequence of the input genome against any number of other genomes, finally forming multiple alignments in MAF blocks. Module 3(post processing): The post-processing part of the pipeline adds context to the RNAs, which in many cases will allow for a curation of the structured RNA loci. The numbers in parenthesis are those obtained after the removal of 34 annotations as part of the curation procedure: 12 tRNAs, 15 homology based miRNAs, and 7 de novo miRNAs.

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