Research article
Considerations in the identification of functional RNA structural elements in genomic alignments
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* Corresponding author: Timothy R Hughes t.hughes@utoronto.ca
1 Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, 160 College St, Toronto, ON M5S 3E1 Canada
2 Department of Medical Genetics and Microbiology, 10 King's College Circle, Toronto, ON M1R 4F9 Canada
BMC Bioinformatics 2007, 8:33 doi:10.1186/1471-2105-8-33
Published: 30 January 2007Additional files
Additional File 7:
ncRNA set. Set of human, mouse, fly, worm, and yeast ncRNAs used to compile the test set.
Format: XLS Size: 1.1MB Download file
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Additional File 8:
ncRNA alignment test set. 3046 eukaryotic ncRNA pairwise alignments.
Format: TAB Size: 625KB Download file
Additional File 3:
Shuffles pairwise alignments while preserving dinucleotides (in both sequences), base composition, gaps, and local conservation.
Format: PL Size: 8KB Download file
Additional File 1:
Precision-recall plots for individual ncRNA classes (Supplementary Figures 1 through 8). Dependency of precision and recall on score threshold and level of conservation (as per Figure 2).
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Additional File 2:
Supplementary Table 1. Detailed results on test set for EvoFold with and without members of the EvoFold training set.
Format: XLS Size: 19KB Download file
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Additional File 9:
high-scoring sequence windows from chromosome 19. Human strands shown. Some are shorter than 120 bases due to the presence of gaps in the human genome sequence.
Format: XLS Size: 2.4MB Download file
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Additional File 5:
Extracts portions of UCSC pairwise genomic alignments. Takes as input genomic coordinates (BED file format) and alignment files and outputs alignments for coordinates where alignments exist.
Format: PL Size: 5KB Download file
Additional File 6:
Extracts portions of UCSC multiple genomic alignments (human 8-way). Takes as input human genomic coordinates (BED file format) and alignment files and outputs alignments where possible (i.e. alignments exist).
Format: PL Size: 6KB Download file
Additional File 4:
Script that calculates thermodynamic stability z-score using MFOLD (see Table 1).
Format: PL Size: 3KB Download file