RBLOSUM performs better than CorBLOSUM with lesser error per query

Abstract

Abstract Objective BLOSUM matrices serve as standard matrices for many protein sequence alignment programs. BLOSUM matrices have been constructed using BLOCKS version5.0 with 27,102 BLOCKS, whereas the latest updated version14.3 has 6,739,916 BLOCKS. We read with interest the research article by Hess et al. (BMC Bioinform 17:189, 2016) on CorBLOSUM, wherein it is argued that an inaccuracy in the BLOSUM code affects the cluster memberships of sequences. They show that replacing the integer based clustering threshold to floating point arguably improves the performances of CorBLOSUM over BLOSUM and RBLOSUM matrices. They compare BLOSUM6214.3 against RBLOSUM69, with relative entropies of 0.2685 and 0.2662 respectively. The present work attempts to repeat the computation to verify the respective analog matrices. Results In our attempt to repeat the computation, we observed that the relative entropy of BLOSUM6214.3 is 0.2360 and BLOSUM5014.3 is 0.1198. As only matrices of similar entropies can be compared, BLOSUM62 can be compared only with RBLOSUM66 and BLOSUM50 can be compared only with RBLOSUM56. We conducted experiments with Astral data sets, and demonstrated the improved accuracy in the coverage. Our results imply that RBLOSUM performs statistically better than CorBLOSUM and BLOSUM matrices.

Keywords

• Substitution matrix
• Sequence similarity search
• BLOSUM
• RBLOSUM
• CorBLOSUM