Final answer:
When reviewing a BLASTX alignment in DSAP, it is important to assess the alignment scores, the Expected value (E-value), and the percentage of conservation, ensuring that the sequence alignment is statistically significant and that the amino acids conserved align with expected biological functions or structures.
Step-by-step explanation:
Before progressing to the next page in DSAP when looking at a BLASTX alignment, it is essential to observe key aspects. First and foremost, examine the alignment scores, which denote how well the query sequence matches the subject sequence. Positive scores are granted for nucleotide matches, with mismatches and gaps resulting in penalties. A higher overall score indicates a better alignment.
Moreover, it is crucial to consider the Expected value (E-value). The E-value provides insight into the number of hits one might expect to see by chance with a given word size. An E-value closer to zero suggests a more significant alignment with less likelihood of it being due to random chance. Lastly, evaluate the percentage of conservation to determine the degree of similarity between the query and subject sequences as well as if there is a conservation trend among the amino acids (apolar, polar, or charged).