Better Bonding with Beans

Background: Phylogenetically related miRNAs (miRNA families) convey important information of the function and evolution of miRNAs. Due to the special sequence features of miRNAs, pair-wise sequence identity between miRNA precursors alone is often inadequate for unequivocally judging the phylogenetic relationships between miRNAs. Most of the current methods for miRNA classification rely heavily on manual inspection and lack measurements of the reliability of the results. Results: In this study, we designed an analysis pipeline (the Phylogeny-Bootstrap-Cluster (PBC) pipeline) to identify miRNA families based on branch stability in the bootstrap trees derived from overlapping genome-wide miRNA sequence sets. We tested the PBC analysis pipeline with the miRNAs from six animal species, H. sapiens, M. musculus, G. gallus, D. rerio, D. melanogaster, and C. elegans. The resulting classification was compared with the miRNA families defined in miRBase. The two classifications were largely consistent. Conclusion: The PBC analysis pipeline is an efficient method for classifying large numbers of heterogeneous miRNA sequences. It requires minimum human involvement and provides measurements of the reliability of the classification results. Background MicroRNAs (miRNAs) are small (~22 nucleotides) noncoding RNAs that have the ability to repress the expression of target genes post-transcriptionally. Since the discovery of the first two miRNA genes, lin-4 [1,2] and let-7 [3,4], much has been learned about the structure, biogenesis and function of miRNAs [5-7]. A growing number of miRNAs have been found in animals, plants and viruses [8,9]. The "miRBase" database [10] currently hosts 4039 miRNAs from 45 species (Release 8.2). Studies in plants [11], animals [12,13], and viruses [8] have shown that the innovation of miRNAs is an ongoing process [14,15], which indicates that most miRNAs are of different evolutionary origins. Some miRNAs, however, were also populated through local or genome-wide duplications [14,16], and formed miRNA families. As the phylogenetically related miRNAs convey important information about the function and evolution of miRNAs, a reliable classification of miRNA families is indispensable for miRNA studies. Published: 6 March 2007 BMC Genomics 2007, 8:66 doi:10.1186/1471-2164-8-66 Received: 28 October 2006 Accepted: 6 March 2007 This article is available from: http://www.biomedcentral.com/1471-2164/8/66 © 2007 Huang and Gu; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.