Question

How come the scores are a lot less and the E-values not as good for a BLASTX search as for the BLASTN?

Answer 1

BLASTX gives fewer matches and lower E-values compared to BLASTN because it aligns protein sequences while BLASTN aligns nucleotide sequences.

Step-by-step explanation:

The BLASTX search typically gives fewer matches and lower E-values compared to BLASTN because BLASTX is used to align protein sequences while BLASTN aligns nucleotide sequences. Here's why:

1. BLASTX searches for matches in protein databases using a nucleotide query sequence. In this search, the query sequence is translated into all possible reading frames, which leads to fewer matches because protein sequences are usually more conserved compared to nucleotide sequences.
2. On the other hand, BLASTN searches for matches in nucleotide databases using a nucleotide query sequence. Since the nucleotide sequences are directly aligned, it can result in more matches.