The ESTs orientations were not considered in the analysis.
Based on the tag-to-gene matching strategy described above it was found that 24.3% of all matched tags matched A. thaliana genes via oriented Brassica ESTs in antisense orientation (corresponding to 1762 of 5,120, 34.4% of all matched genes, Table 2).
To differentiate between tags that matched B. napus seed transcripts in sense and in antisense orientation, the oriented sense EST dataset was used in combination with an oriented reverse-complemented EST dataset (antisense EST dataset).
In addition, a large set of MPSS signatures that matched to the anti-sense orientation ESTs was identified.
At 35 DAP the most abundantly expressed tags were matched via Brassica ESTs in sense orientation to the four A. thaliana 2S seed storage proteins 1 4 (napins) AT4G27140, AT4G27250, AT4G27160 and AT4G27170 (37,182 to 41,806 tags per million).
The location of the potential miRNAs varied among ESTs, 4 were found in the sense orientation of the EST, 1 was found in the antisense orientation.
To perform our analysis we relied on information about the orientation of EST sequence data.
Due to their orientation, these ESTs could represent an antisense transcript of the alternative exon of Pdcd2.
Because of the problematic assignment of the orientation of ESTs, unambiguous sequences corresponding to the gau region are rare in the database.
Based on the cDNA library production using polyA+ trapped mRNA, LongSAGE tags are expected to match at the anchoring enzyme site closest to the 3' end of full-length ESTs expressed in sense orientation (canonical position).
