Question

What would cause a difference in the results shown below of the best matches between the BLASTX and the BLASTP? (Check all that apply)

1. The BLASTX query sequence was translated in all six reading frames, while the BLASTP query sequence was only translated in the correct reading frame.
2. The BLASTX database was a protein database, while the BLASTP database was a nucleotide database.
3. The BLASTX query sequence was a nucleotide sequence, while the BLASTP query sequence was a protein sequence.
4. The BLASTX search was performed using a different scoring matrix than the BLASTP search.
5. The BLASTX search was performed using a different e-value cutoff than the BLASTP search.

Answer 1

BLASTX and BLASTP may yield different results due to BLASTX translating nucleotide sequences in all six reading frames and BLASTP using only the correct frame, BLASTX queries being nucleotides and BLASTP queries proteins, and differences in scoring matrices and e-value cutoffs used.

Step-by-step explanation:

Differences in the results of BLASTX and BLASTP can be attributed to several factors. Firstly, option 1 suggests that BLASTX considers all six possible reading frames for a nucleotide sequence, while BLASTP assumes the query sequence is in the correct reading frame. Secondly, option 3 highlights that BLASTX uses a nucleotide sequence which it translates into a protein sequence, contrasting with BLASTP, which uses a protein sequence as its query. Lastly, differences in algorithms, such as using different scoring matrices (option 4) or e-value cutoffs (option 5), could influence the search outcomes.

It is crucial to note that option 2 is incorrect because both BLASTX and BLASTP searches are performed against protein databases.