Information Technology Reference
In-Depth Information
Table 4.3 Reference-dependent alignment recall on the large benchmark Set60K
HMMER (%) HHalign (%) MRFalign (%)
Family 57.4 69.2 71.0
Superfamily 31.2 42.0 48.1
Fold 1.3 7.0 14.2
Family (beta) 60.9 69.9 73.1
Superfamily (beta) 35.0 47.2 52.1
Fold (beta) 2.5 8.3 17.3
Only exact matches are considered as correct in evaluating alignment quality. The test protein pairs
are divided into 3 groups based upon the SCOP classification. The bold indicates the best results.
The structure alignments generated by TMalign are used as reference alignments
Table 4.4 Reference-dependent alignment recall on the large benchmark Set60K
HMMER (%) HHalign (%) MRFalign (%)
Family 59.1 70.5 74.5
Superfamily 32.3 42.4 51.7
Fold 1.6 8.0 15.5
Family (beta) 64.0 75.1 78.4
Superfamily (beta) 37.0 50.2 55.8
Fold (beta) 3.0 9.1 17.1
The structure alignments generated by Matt are used as reference alignments. See Table 4.3 for
more explanation
Table 4.5 Reference-dependent alignment recall on the large benchmark Set60K
HMMER (%) HHalign (%) MRFalign (%)
Family 63.2 72.6 75.5
Superfamily 32.8 49.4 55.6
Fold 2.0 8.7 18.4
Family (beta) 68.4 79.0 82.9
Superfamily (beta) 39.1 52.9 60.7
Fold (beta) 4.0 10.1 21.8
The structure alignments generated by DeepAlign are used as reference alignments. See Table 4.3
for more explanation
by
18 %, respectively. At the fold level, MRFalign outperforms HHalign
and HHMER by
*
6 and
*
14 %, respectively.
Alignment recall for beta proteins As shown in Tables 4.3 , 4.4 and 4.5 , our
method MRFalign outperforms HHalign and HMMER by * 3 and * 12 %,
respectively, at the family level;
*
7 and
*
7 and
19 %, respectively, at the superfamily
*
*
level; and
10 and
16 %, respectively, at the fold level, regardless of reference
*
*
alignments.
Search WWH ::




Custom Search