AspicDB transcript predictions were retrieved from version 2 (December 2009) [ 13].
The positions of predicted (annotated) exons were retrieved from version 63 of the Ensembl database (Flicek et al. 2011) for all species except sheep.
A full-length sequence of the intein was then retrieved from version 2 of the C. reinhardtii genome sequence assembly, available from the Joint Genome Institute [ 33].
Annotated protein sequences for ten different species were retrieved from version 2.5 of the PLAZA protein database [ 33] and four external proteins sets, from conifer species, were also included (Table 1).
Exon positions for all genes were retrieved from version 57 of the Ensembl database (Flicek et al. 2011), except for sheep for which CDS positions were downloaded from http://www.livestockgenomics.csiro.au/sheep/ (ISGC et al. 2010).
The theft "was carefully thought out, cleverly conceived and it was quickly executed, so that suggests professionals," said Charles Hill, a retired Scotland Yard art detective turned private investigator who went undercover to retrieve a version of "The Scream," by Edvard Munch, after it was stolen in 1994 in Oslo.
Gene annotation tables of the three species were retrieved from FlyBase (version 2012_06) with individual versions 5.48, 1.3 and 1.3 for D. melanogaster, D. simulans and D. sechellia, respectively.
Tandem mass spectra were retrieved using Xcalibur (version 2.2, Thermo Fisher Scientific) and AnalystTF (version 1.6, AB SCIEX) software.
Annotations for Arabidopsis thaliana (including mRNAs, TE fragments, cDNAs, ESTs and T-DNA insertion sites) and Oryza sativa were retrieved from TAIR (version 10, http://www.arabidopsis.org/) [ 31] and RGAP (version 7, http://rice.plantbiology.msu.edu/) [ 57], respectively.
The known microRNA genes were obtained from miRBase (version 17.0) [ 41] and the experimentally verified MREs were downloaded or retrieved from TarBase (version 4.0) [ 35] and miRTarBase (release 2.5) [ 36].
