I have came across a confusing situation while doing BLAST. blastn did not show any matches with my query sequence even though I shuffle the parameters.
Dear Maria,
A nucleotide sequence consists of only four nucleotides: A,G,C and T or U, while a protein sequence has 20 amino acids. Thus the sensitivity of nucleotide blast for distantly related sequences is very low, or non-existent, while this is not the case for protein sequences. May I recommend my chapter "Phylogenetic analysis using protein sequences" that discusses this problem in detail? It can be downloaded from ResearchGate by using the following link: https://www.researchgate.net/publication/326294021_Phylogenetic_analysis_using_protein_sequences?_iepl%5BviewId%5D=8kPy1eLh1LEysebXTTMvGme9&_iepl%5Bcontexts%5D%5B0%5D=projectUpdatesLog&_iepl%5BtargetEntityId%5D=PB%3A326294021&_iepl%5BinteractionType%5D=publicationTitle
due to presence of more than one codon that code one amino acid as in leucine which can results from 6 codons
Yes that's one reason and the other is that DNA/RNA has only 4 letters, while protein has 20 amino acids.
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