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).
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