Objective: BLOSUM matrices serve as standard matrices for many protein sequence alignment programs. BLOSUM matrices have been constructed using BLOCKS version with 27,102 BLOCKS, whereas the latest updated version 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 BLOSUM62 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 BLOSUM62 is 0.2360 and BLOSUM50 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.
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| http://dx.doi.org/10.1186/s13104-018-3415-5 | DOI Listing |
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