Abstract
Verification of the PREFAB database containing golden standard protein alignments was performed. It has revealed a significant number of differences between the sequences from PREFAB and PDB databases. It was shown that, compared with the sequences given in the PDB, 575 alignments referred to a sequence with a gap; such alignments were excluded. Furthermore, compared with the PDB sequences, single substitutions or insertions were found for 440 amino acid sequences from PREFAB; these sequences were edited. SCOP domain analysis has shown that only 502 alignments in the resulting set contain sequences from the same family. Finally, eliminating duplicates, we have created a new golden standard alignment database PREFAB-P based on PREFAB; the PREFAB-P database contains 581 alignments.
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Original Russian Text © T.V. Astakhova, M.N. Lobanov, I.V. Poverennaya, M.A. Roytberg, V.V. Yacovlev, 2012, published in Biofizika, 2012, Vol. 57, No. 2, pp. 205–211.
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Astakhova, T.V., Lobanov, M.N., Poverennaya, I.V. et al. Verification of the PREFAB alignment database. BIOPHYSICS 57, 133–137 (2012). https://doi.org/10.1134/S0006350912020030
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DOI: https://doi.org/10.1134/S0006350912020030