Sentence examples for predictions were downloaded from inspiring English sources

N-SCAN and Augustus predictions were downloaded from the UCSC Genome browser [ 43, 44] and SNAP predictions were downloaded from [ 45].

Venn Diagrams were generated using Venny [ 74]. miRNA target predictions were downloaded from TargetScan Human Release 5.2, with predicted target genes for miR-181b and miR-107 categorised by cross-species conservation and seed-region composition before being correlated against the observed gene expression changes subsequent to miRNA modulation.

TWINSCAN and TWINSCAN_EST predictions were downloaded from http://mblab.wustl.edu/.edu/

For OMA (Altenhoff et al. 2011), ortholog predictions were downloaded from omabrowser.org (December 2012 release).

The Apis mellifera protein set (OGS2) and abinitio gene predictions were downloaded from BeeBase.

The most recently updated predictions were downloaded, with year that those predictions were released indicated in parentheses.

A prerelease of Medicago truncatula genome (December 14, 2006), including gene predictions, was downloaded from http://www.medicago.org/.org/

PicTar prediction was downloaded from UCSC genome browser PicTar miRNA track.

DNA methylation data generated by Iwamoto et al., used to validate CETS model prediction was downloaded from GEO accession.

Once the regions were determined, gene models (predicted by the Gnomon gene prediction tool) were downloaded using BioMart that were subsequently annotated using the P. trichocarpa version 3 annotation information.

We used two complete lists of human miRNA targets published by Lewis et al. and Krek et al. These miRNA target prediction datasets were downloaded from the most recently updated websites.