8.13 Look for Stop Codons and Frame-Shifts to find Pseudo-Genes

Stop codons generally aren't found in protein-coding genes. They are common, however, in pseudo-genes. It's important to recognize pseudo-genes early in a sequence-analysis pipeline because they may confound downstream analyses. Pseudo-genes usually have stop codons and insertions or deletions (Figure 8-5). Stop codons are easy to spot in alignments, but insertions and deletions must be inferred from alignment coordinates. Look for HSPs that are in different frames and appear too close to be separated by an intron (< 25 bp).

Figure 8-5. BLASTX alignment of a pseudo-gene (stop codons are circled)