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(superfamily) level. For each query protein, we examine the top 1-, 5- and 10-
ranked proteins, respectively.
As shown in Table
4.11
, tested on SCOP20, SCOP40 and SCOP80 at the
superfamily level, our method MRFalign succeeds on
6,
4 and
4 % more
*
*
*
query proteins than HHsearch, respectively, when only the
first-ranked proteins are
considered. As shown in Table
4.11
, at the fold level, MRFalign succeeds on
11,
*
rst-
ranked proteins are evaluated. At the superfamily level, SCOP20 is more chal-
lenging than the other two benchmarks because it contains fewer proteins similar at
this level. Nevertheless, at the fold level, SCOP80 is slightly more challenging than
the other two benchmarks maybe because it contains many more irrelevant proteins
and thus, the chance of ranking false positives at top is higher.
Similar to alignment accuracy, MRFalign for homology detection also has a
larger advantage on the beta proteins. In particular, as shown in Table
4.13
, tested
on SCOP20, SCOP40 and SCOP80 at the superfamily level, MRFalign succeeds on
*
11 and
12 % more proteins than HHsearch, respectively, when only the
*
*
rst-
ranked proteins are evaluated. As shown in Table
4.12
, at the fold level, MRFalign
succeeds on
7,
*
5 and
*
7 % more proteins than HHsearch, respectively, when only the
*
13,
*
16 and
*
17 % more proteins than HHsearch, respectively,
when only the
first-ranked proteins are evaluated. Note that in this experiment, only
the query proteins are mainly-beta proteins, the subject proteins may be of any
types. If we restrict the subject proteins to only beta proteins, the success rate
increases further due to the reduction of false positives (Table
4.14
).
Table 4.11 Homology detection success rate (%) at the superfamily level on three benchmarks
SCOP20, SCOP40 and SCOP80
SCOP20
SCOP40
SCOP80
Top1
Top5
Top10
Top1
Top5
Top10
Top1
Top5
Top10
Hmmscan
35.2
36.5
36.5
40.2
41.7
41.8
43.9
45.2
45.3
FFAS
48.6
54.4
55.6
52.1
56.3
57.1
49.8
53.0
53.7
HHsearch
51.6
57.3
59.2
55.8
60.8
62.4
56.1
60.1
61.8
HHblits
51.9
56.3
57.5
56.0
59.8
60.9
59.2
62.5
63.3
MRFalign
58.2
61.7
63.4
59.3
63.6
65.8
60.4
64.7
66.1
Table 4.12 Homology detection success rate (%) at the fold level on three benchmarks SCOP20,
SCOP40 and SCOP80
SCOP20
SCOP40
SCOP80
Top1
Top5
Top10
Top1
Top5
Top10
Top1
Top5
Top10
Hmmscan
5.2
6.1
6.1
6.2
6.9
6.9
5.9
6.5
6.6
FFAS
13.1
18.7
20.0
10.4
14.5
15.4
9.1
11.9
12.6
HHsearch
16.3
24.7
28.6
17.6
25.3
29.1
15.4
21.9
25.0
HHblits
17.4
25.2
27.2
19.1
26.0
28.2
18.4
25.0
27.0
MRFalign
27.2
36.8
41.2
28.3
37.9
42.4
27.0
38.1
41.6
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