Question

What are some of the strengths of BLASTp searching and Conserved Domain searching for protein annotation? What are some of the weaknesses?

Answer 1

BLAST is the method for comparing sequences of biological molecules like DNA sequence or amino acid sequences.

BLASTp is used for protein sequence to protein database blast or sequence alignment.

The advantage is it used annotated proteins and hence is much more sensitive than BLASTn which searches the nucleotide sequences. This is because there are 20 amino acids present for 64 possible codons, so there is a degree of degeneracy. SO for a functional searching searching at protein level (amino acids) would be much more sensitive than and alighnment at nucleotide level.

Its weakness is if misses any gene which are not annotated and not in protein database. The protein database is often not as comprehensive as nucleotide sequence.