Questions in BLASTn and BLASTp

Question

[mangfu100]

Hi all.

I am doing BLAST to identify sequence similarity.

I queried my data into databases and I got my results using blastp. After then, I also tried to do blastn in order to check sequence level similarities. However, I don't get it which search is more informative.

Could you tell me about its characterization?

Answer 1

[Ram]

The core comparison-based information content is almost the same, but you are right in assuming that comparing proteins is intrinsically more informative than comparing nucleotides. The reason for this is that amino acids can be grouped into classes, and weights can be attributed based on if the change results in a class change. For example, an Arginine to a Lysine mutation (amino acids with basic side chains, both) is definitely less damaging/destabilizing than an Arginine to a Tryptophan mutation, in most cases.

Nucleotide changes have lesser context by themselves and are hence less informative of their own.

Protein comparison in BLAST is also augmented by factors such as discovering putative domains in the query protein by aligning its segments to its nearest neighbors, iterative searches branching out and giving us an evolutionary sense, comparison to known structures to model the structure of a protein with unknown structure, etc. All of this stems from the fact that a sequence of amino acids is intrinsically more informative than a sequence of nucleotides. This has nothing to do with blastn and blastp.

Answer 2

[thorerges]

I am sorry, I think you need to read how both these algorithms work:

http://www.ncbi.nlm.nih.gov/BLAST/blast_program.shtml

• blastp: compares an amino acid query sequence against a protein sequence database
• blastn: compares a nucleotide query sequence against a nucleotide sequence database

Hope this helps.