The BlastNP: a novel, sensitive sequence similarity searching method using overlappingly translated sequences

Abstract

An alternative method to TblastX has been developed, known as blastNP. Nucleic acids in database and query sequences were translated into overlapping protein-like sequences (overlappingly translated sequences or OTSs) before searching with blastP. Thus, each nucleic acid sequence is represented by a single "protein like" sequence (instead of three hypothetical proteins in different reading frames). The BlastNP method is defined as a BlastP that is performed on an overlappingly translated nucleic acid database using a similarly converted nucleic acid query. The specificity and sensitivity of blastNP and TblastX is quantitatively very similar, except that blastNP is more sensitive to detect short sequence similarities (less than 50 residues). However, a qualitative comparison of the observed similarities showed that only 56% was detected by both methods, but 22% was indicated only by blastNP and 22% only by TblastX. For example, a statistically significant similarity between prion protein (PrP) and transcriptions factors (TF) was only detected by blastNP. A signal amplification was seen when OTS sequences were used in similarity visualisation methods (like LALIGN) instead of nucleic acids.