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. 2013 Jun;23(6):1018–1027. doi: 10.1101/gr.137091.111

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© 2013, Published by Cold Spring Harbor Laboratory Press

This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 3.0 Unported License), as described at http://creativecommons.org/licenses/by-nc/3.0/.

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Figure 1. — The whole-genome REAPR (RE-Alignment for Prediction of structural ncRNAs) pipeline. Step 1: The syntenic blocks of the WGA are sliced into windows, which are filtered by thermodynamic stability. Stable windows of the same orientation are merged into stable loci. Step 2: Each candidate locus is realigned based on sequence and structure similarity by LocARNA within limited deviation from the WGA. Step 3: Each realigned locus is evaluated by a de novo ncRNA predictor such as RNAz 2.0 for its likelihood of containing structural ncRNA. The evaluation is then transformed into a q-value to control FDR.