To test this possibility the mRNA sequences of the 554 genes containing the motif in downstream position, were retrieved from the UCSC Genome Browser (http://genome.ucsc.edu/) and analyzed for their translation initiation site as specified by the database.
Gene annotation, (e.g. Ensembl gene id, chromosome, strand, start and end position) was retrieved through BiomaRt R/Bioconductor package [ 32].
A read was considered as correctly mapped if among the reported hits at least one hit fitted the following criteria: i) the original start position (i.e. the position from which the read is generated) was retrieved, ii) the end position was retrieved, and iii) the alignment produced by the mapper showed exactly the same number of insertions, deletions, and substitutions.
With the eyes closed, the subject was asked to rotate the head "as far as comfortable" towards the left, and then reposition the head to the starting position and give a verbal signal when he/she thought that the starting position was retrieved.
The histone binding pattern nearby the TSSs of all protein coding genes is retrieved as positive set, and the ones of 10,000 random positions are retrieved as negative set.
In other species, the transcriptional start positions were retrieved in the literature [ 20, 35, 60- 77].
Tryptophan tRNA positions were retrieved in each genome by a manual search of GenBank annotation files.
Two kilobases of sequence surrounding the summit positions were retrieved for each summit set.
Map positions were retrieved from the current bovine genome sequence assembly map of BTA6 at NCBI (Btau build 4.0 [ 31]).
Orthologs of these genes in the human, rat, and dog genomes, along with their genomic positions, were retrieved using Ensembl BioMart homology filters.
