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Journal of Nucleic Acids
Volume 2010 (2010), Article ID 495904, 10 pages
http://dx.doi.org/10.4061/2010/495904
Research Article

NOVOMIR: De Novo Prediction of MicroRNA-Coding Regions in a Single Plant-Genome

Institut für Physikalische Biologie, Universitätsstr. 1, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany

Received 25 March 2010; Revised 10 June 2010; Accepted 29 June 2010

Academic Editor: Ben Berkhout

Copyright © 2010 Jan-Hendrik Teune and Gerhard Steger. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Supplementary Material

Fig. S1: Length distribution of plant pre‐miRNA in different versions of mirBase.

Fig. S2: Nucleotide composition of plant pre-miRNAs and mature miRNAs in different versions of miRBase.

Fig. S3: Nucleotide distribution in mature plant miRNAs from mirBase version 14.

Fig. S4: Minimum of free energy (in kcal/mol) of secondary structures of plant pre-miRNA in mirBase version 14.

Fig. S5: Workflow in novoMIR.

Fig. S6: Hidden‐Markov model used for classification.

Fig. S7: Expression pattern of ath-MIR842a viewed in the ASRP browser.

Fig. S8: Expression pattern of a pre-miRNA candidate viewed in the ASRP browser.

Fig. S9: Expression pattern of a pre-miRNA candidate viewed in the ASRP browser.

Fig. S10: Expression pattern of a pre-miRNA candidate viewed in the ASRP browser.

Fig. S11: Expression pattern of a pre-miRNA candidate viewed in the ASRP browser.

Table S1: Comparison of novoMIR's sensitivity for detecting plant pre‐miRNAs from different versions of mirBase.

  1. Supplementary Material