In silico miRNA prediction in metazoan genomes: balancing between sensitivity and specificity

doi:10.1186/1471-2164-10-204

BMC Genomics

Volume 10

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Research article

In silico miRNA prediction in metazoan genomes: balancing between sensitivity and specificity

Ate van der Burgt¹^,2 , Mark WJE Fiers¹^,4 , Jan-Peter Nap¹^,3 and Roeland CHJ van Ham¹^,2

¹Applied Bioinformatics, Plant Research International, Wageningen University & Research Centre, PO Box 16, 6700 AA Wageningen, The Netherlands

²Laboratory of Bioinformatics, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands

³Centre for BioSystems Genomics 2012 (CBSG2012), PO Box 98, 6700 AB Wageningen, The Netherlands

⁴Current address: New Zealand Institute for Plant & Food Research Ltd, Private Bag 4704, Christchurch, New Zealand

author email corresponding author email

BMC Genomics 2009, 10:204doi:10.1186/1471-2164-10-204


Published:	30 April 2009

Additional files

Additional file 1:

Data fit of descriptors. Results of the data fit for 40 descriptors from the taxonomic set Metazoa (3,902 miRNA hairpins).

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Additional file 2:

Detailed explanation of descriptors. A set of 40 potentially discriminative features of miRNA hairpins, referred to as descriptors, was defined and includes both physical and sequence characteristics of miRNA hairpins.

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Additional file 3:

Descriptor interdependency. Correlation among descriptors in their S<1 fractions, assessed by Cohen's kappa coefficient κ of all 780 possible pairs of descriptors, using the miRNA hairpins of the taxonomic set Metazoa.

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Additional file 4:

Taxonomic sets with at least 100 miRNA sequences. MiRNA sequences were divided in hierarchically organized subsets based on their taxonomic relationships. A total of 23 taxonomic sets comprised at least 100 sequences and were used for analysis.

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Additional file 5:

Hairpins identified in Epstein-Barr Virus. Details of 23 hairpins with L score = 1.0, identified in Epstein-Barr Virus [EMBL: AJ507799] for the scoring model Metazoa.

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Additional file 6:

Hairpins identified in Mareks disease Virus. Details of 18 hairpins with L >= 0.30 identified in Mareks Disease Virus [EMBL: AF243438] for the scoring model Metazoa.

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Additional file 7:

Hairpin loci in C. elegans obtained by the filtering protocol "Clustered". Filtering on L score was combined with filtering on genomic context, a protocol referred to as "Clustered".

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Additional file 8:

Hairpin loci in C. elegans obtained by the filtering protocol "Similar". Filtering on L score was combined with filtering on a similarity threshold to known metazoan mature miRNAs, a protocol referred to as "Similar".

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Additional file 9:

Performance of the scoring model Metazoa. Analysis of the performance of the scoring model Metazoa on sets of genomic hairpins other than those derived for the C. elegans genome.

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Additional file 10:

MiRNAs that excluded from the analyses. The hairpin structure of six sequences deviated considerably from the predicted characteristics of miRNA hairpins and were excluded from all subsequent analyses.

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