Table 1 |
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|
Predictor performance |
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|
GB |
- IS |
+ IS |
Manual |
|
|
|
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|
A. dehalogenans 2CPC (NC_007760) |
||||
|
Total IS ORF |
1 |
4 |
4 |
2 |
|
Complete ORF |
- |
0 |
0 |
0 |
|
Partial ORF |
- |
1 |
1 |
1 |
|
Pseudogene |
1 |
2 |
2 |
1 |
|
Unknown ORF |
- |
1 |
1 |
0 |
|
Total IS |
- |
4 |
4 |
2 |
|
Different IS |
- |
4 |
4 |
2 |
|
Anaeromyxobacter sp. Fw109 5 (NC_009675) |
||||
|
Total IS ORF |
15 |
22 |
24 |
19 |
|
Complete ORF |
- |
4 |
12 |
12 |
|
Partial ORF |
- |
1 |
2 |
6 |
|
Pseudogene |
1 |
4 |
4 |
1 |
|
Unknown ORF |
- |
13 |
6 |
0 |
|
Total IS |
- |
20 |
21 |
16 |
|
Different IS |
- |
16 |
17 |
12 |
|
Anaeromyxobacter sp. K (NC_011145) |
||||
|
Total IS ORF |
14 |
25 |
28 |
27 |
|
Complete ORF |
- |
12 |
26 |
26 |
|
Partial ORF |
- |
2 |
0 |
0 |
|
Pseudogene |
- |
1 |
1 |
1 |
|
Unknown ORF |
- |
10 |
1 |
0 |
|
Total IS |
- |
19 |
19 |
18 |
|
Different IS |
- |
10 |
10 |
9 |
|
A. dehalogenans 2CP1 (NC_011891) |
||||
|
Total IS ORF |
15 |
33 |
35 |
35 |
|
Complete ORF |
- |
18 |
24 |
27 |
|
Partial ORF |
- |
4 |
2 |
3 |
|
Pseudogene |
- |
8 |
8 |
5 |
|
Unknown ORF |
- |
3 |
1 |
0 |
|
Total IS |
- |
25 |
25 |
23 |
|
Different IS |
- |
12 |
12 |
14 |
|
A. aeolicus VF5 (NC_000918) |
||||
|
Total IS ORF |
- |
7 |
7 |
3 |
|
Complete ORF |
- |
0 |
2 |
2 |
|
Partial ORF |
- |
1 |
1 |
1 |
|
Pseudogene |
- |
0 |
0 |
0 |
|
Unknown ORF |
- |
6 |
4 |
0 |
|
Total IS |
- |
7 |
7 |
3 |
|
Different IS |
- |
6 |
6 |
2 |
|
C. thermocellum 27405 (NC_009012) |
||||
|
Total IS ORF |
75 |
143 |
144 |
160 |
|
Complete ORF |
- |
81 |
123 |
125 |
|
Partial ORF |
- |
43 |
11 |
27 |
|
Pseudogene |
- |
7 |
7 |
8 |
|
Unknown ORF |
- |
12 |
3 |
0 |
|
Total IS |
- |
115 |
115 |
119 |
|
Different IS |
- |
27 |
27 |
26 |
|
S. maltophilia R5513 (NC_011071) |
||||
|
Total IS ORF |
11 |
21 |
22 |
20 |
|
Complete ORF |
- |
13 |
19 |
19 |
|
Partial ORF |
- |
7 |
1 |
1 |
|
Pseudogene |
- |
1 |
1 |
0 |
|
Unknown ORF |
- |
0 |
1 |
0 |
|
Total IS |
- |
18 |
19 |
16 |
|
Different IS |
- |
6 |
7 |
4 |
|
S. maltophilia K279a (NC_010943) |
||||
|
Total IS ORF |
49 |
53 |
54 |
57 |
|
Complete ORF |
- |
18 |
45 |
47 |
|
Partial ORF |
- |
27 |
5 |
9 |
|
Pseudogene |
- |
3 |
3 |
1 |
|
Unknown ORF |
3 |
5 |
1 |
0 |
|
Total IS |
- |
38 |
39 |
36 |
|
Different IS |
- |
18 |
19 |
18 |
|
|
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|
The table shows a comparison of IS annotations of eight bacterial genomes contained in the corresponding GenBank files (GB) with those obtained by manual annotation (Manual) and using the ISsaga predictor with two different IS reference databases. In one database (-IS) the reference ISs contained in the genome under test were removed while in the other these ISs were included (+IS). The total number of IS-associated ORFs (Total IS ORF) are divided into four categories: Complete ORFs, Partial ORFs, Pseudogenes and Unknown. The category 'Unknown' includes all examples that cannot be distinguished by the predictor as complete or partial due to the absence of sufficient numbers of closely related examples in the reference database. The categories 'Total IS' and 'Different IS' are based on nucleotide predictions. In these predictions the number of ORFs carried by the IS are taken into account. For example, if an IS includes two ORFs, this will be counted as two examples in 'Complete ORF' but as a single IS in 'Total IS'. |
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|
Varani et al. Genome Biology 2011 12:R30 doi:10.1186/gb-2011-12-3-r30 |
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