Open Access Highly Accessed Research article

MicroRNAs and essential components of the microRNA processing machinery are not encoded in the genome of the ctenophore Mnemiopsis leidyi

Evan K Maxwell12, Joseph F Ryan13, Christine E Schnitzler1, William E Browne4 and Andreas D Baxevanis1*

Author Affiliations

1 Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA

2 Bioinformatics Program, Boston University, Boston, MA, 02215, USA

3 Sars International Center for Marine Molecular Biology, University of Bergen, Bergen, 5008, Norway

4 Department of Biology, University of Miami, Coral Gables, FL, 33146, USA

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BMC Genomics 2012, 13:714  doi:10.1186/1471-2164-13-714

Published: 20 December 2012

Additional files

Additional file 1:

Dataset 1. contains a folder of source data files (i.e., protein sequence alignments and NEWICK formatted trees containing bootstrap support and Bayesian posterior probabilities, respectively) in plain text format to accompany the phylogenetic trees produced for Figure 3 and Additional file 2: Figure S1.

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Additional file 2:

Figure S1. provides a phylogenetic tree, and the corresponding most parsimonious evolutionary scenario, produced on the data used in Figure 3 with the addition of eubacterial sequences, addressing the less parsimonious scenario of Drosha’s direct evolution from eubacterial RNase III enzymes [10].

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Additional file 3:

Dataset 2. contains a folder of output data files in plain text format related to the miRNA predictions (both canonical and mirtron) produced by the various programs described in the Methods.

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Additional file 4:

Figure S2. provides the prediction score histograms produced by the mirtron prediction method used [51].

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Additional file 5:

Figure S3. shows the intron length distribution for Mnemiopsis leidyi.

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Additional file 6:

Figures S4-S8. illustrate the top five mirtron preditions based on the criteria described in the Methods.

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Additional file 7:

Table S1. defines the RNase III protein sequence identifiers used in the phylogenetic trees described above

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