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Citation
Huang, Y., Gu, X. (2007). A bootstrap based analysis pipeline for efficient classification of phylogenetically related animal miRNAs.  BMC Genomics 8(): 66.
FlyBase ID
FBrf0201262
Publication Type
Research paper
Abstract

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.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.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.

PubMed ID
PubMed Central ID
PMC1832191 (PMC) (EuropePMC)
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Secondary IDs
    Language of Publication
    English
    Additional Languages of Abstract
    Parent Publication
    Publication Type
    Journal
    Abbreviation
    BMC Genomics
    Title
    BMC Genomics
    Publication Year
    2001-
    ISBN/ISSN
    1471-2164
    Data From Reference