Abstract: We analyze the quality of the alignment generated by the profile-profile alignment comparison algorithm known as BASIC and compare the results with those obtained with a structural alignment code. By this we compute that a Shannon entropy value > 0.5 gives a sequence to sequence alignment of the target/template couple comparable to that obtained with the structural alignment performed with CE. In our fold recognition/threading code Tangram, the BASIC profile-profile alignment is implemented as follows: 1. The composition profiles PA and PB for the target and template are generated by multiple alignment of the sequences obtained from a three-iteration PSI-BLAST search on the Non-Redundant database (the inclusion threshold is E=10-3). 2. the dot matrix (D) for the profile comparison of two protein sequences D= PTA S PB, (with S=BLOSUM62 substitution matrix) is computed using linear algebra routines. 3. the D matrix is searched for high-scoring alignment by means local Smith-Waterman dynamic programming algorithm. The test set used for the evaluation is composed by 185 template/target couples of PDB structures that share the same SCOP label, but have less than 30% sequence identity When the top-scoring alignments for each target protein in the test set is considered, our BASIC implementation detects the full SCOP label for 125 couples (68%) and generates 114 (62%) alignments with a MaxSub score >=1. Interestingly, it is found that nearly all of the high-quality alignments share a common feature: the average Shannon entropy for the profile sections aligned together is greater than 0.5 for both the template and the target. If only the top scoring alignments for which this condition holds are considered, a subset of 119 alignments is selected, and for 116 of them (97%) the full SCOP label can be assigned to the target, while 108 (91%) gets a nonzero MaxSub score, with an average score of 4.6 MaxSub on the subset On the same 119 couples, the structural alignment program CE computes a nonzero MaxSub score for 116 of them, with an average of 5.7 points. These results indicate that the Shannon entropy value can be used to discriminate a subset of sequence profile-profile alignments of quality comparable to that obtained by means of a structural alignment program.