Fig. 2
From: DECIPHER: harnessing local sequence context to improve protein multiple sequence alignment
C-terminal end of alignments of the lactate/malate dehydrogenase protein family (Pfam [35] accession no. PF00056) colored by predicted secondary structure. The top alignment (sequences named by PDB ID) is from the HOMSTRAD-mod benchmark colored by DSSP assignments [34], with upper-case letters denoting core blocks. The lower alignment shows the same sequences (named by organism) realigned with DECIPHER and colored according to 3-state probabilities predicted by the GOR method [33]. Columns of the lower alignment in bold exactly match columns of the upper reference alignment