Fig. 4
Schematic representation of the algorithms to select putative uORF sequences used for Ka/Ks analysis and to determine the taxonomic range of uORF sequence conservation. Horizontal short black bars depict uORF-tBLASTn and mORF-tBLASTn hit sequences selected in the fourth step of ESUCA. In the fifth step, the uORF-tBLASTn and mORF-tBLASTn hit sequences are classified by orders, using taxonomic lineage information of EST, TSA, and RefSeq RNA sequences from NCBI Taxonomy, and one sequence is selected from each order (See Materials and Methods for the criteria for the selection). The putative uORF sequences in the selected transcript sequences are used for generating the multiple alignments of the uORF amino acid sequences. For Ka/Ks analysis, only putative uORF sequences from orders belonging to Angiospermae are used. In the sixth step of ESUCA, the selected transcript sequences are classified into the 13 plant taxonomic categories to determine the taxonomic range of uORF sequence conservation, using taxonomic lineage information of EST, TSA, and RefSeq RNA sequences