[Verification of the PREFAB alignment database]

The 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 to the sequences given in the PDB database 575 alignments refered to a sequence with a gap; such alignments were excluded. Furthermore, compared to the PDB-sequences a single substitute or the insertions were found for 440 aminoacid sequences from PREFAB database; these sequences were edited. SCOP domain analysis has shown that only 502 alignments in the resulting set contain the 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.