Two methods were used to arrive at our final predicted protein sequence for the RZW gene of Brachypodium distachyon. The first method was an ab initio method. The program FGENESH was used. FGENESH analyzes genomic DNA and comes up with the most likely protein sequence, based on common characteristics of introns and exons. For example, introns start with the nucleotides GT and end with AG. The program also recognizes the start codon, ATG, and the stop codons: TAG, TAA, and TGA. The second method used a program called Phytozome. Phytozome is a DNA library, so it compares the genomic sequence of the RZW gene to known DNA sequences in B. distachyon. It compares the genomic DNA to expressed sequence tags (ESTs), which are overlapping sequences derived from cDNA clones. Because Phytozome compares the RZW gene to known cDNA sequences, its predicted protein sequence is more trustworthy than that of FGENESH.
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