Final answer:
No, the alignments from BLASTx and BLASTp are not always the same, because BLASTx translates nucleotide sequences into protein sequences before alignment, and BLASTp compares protein sequences directly.
Step-by-step explanation:
The start and stop positions of BLASTx and BLASTp alignments are not always the same. BLASTx translates a nucleotide query sequence into protein sequences and then performs the alignment, whereas BLASTp compares protein sequences directly. The differences occur due to the fact that BLASTx takes into account the translation process from DNA/RNA to protein, which can introduce variations not present in the primary protein sequence used in BLASTp. Hence, the alignment may change depending on aspects such as the reading frame chosen for translation in BLASTx. Furthermore, sequence databases like GenBank contain vast amounts of genetic information. Alignments depend on how sequences compare to others available in the databases. Factors like the presence of gaps, which occur when a space is introduced into the sequence alignment to ensure optimal alignment, and word size used by the BLAST algorithm to identify high-scoring pairs can influence the alignment results. Another important concept is the E-value, which indicates the number of hits one can expect by chance when searching a database of a particular size. It helps in determining the significance of the match, with a lower E-value representing a more significant alignment.