Simpulan
Model identifikasi terhadap fragmen metagenome menggunakan PNN dan KNN berhasil dilakukan. Akurasi tertinggi untuk PNN didapat dengan nilai 100%. Percobaan menggunakan panjang yang beragam dengan coverage yang sama tidak memberikan dampak yang signifikan terhadap hasil akurasi. Fragmen dengan panjang 200 bp, 1 Kbp, 3 Kbp dan 10 Kbp adalah sama, yaitu 100%. Dapat dikatakan bahwa seluruh data dapat diklasifikasikan berdasarkan genusnya secara sempurna. Klasifikasi KNN didapat dengan nilai yang sama yaitu 100% untuk semua k. Dalam hal ini diambil k yang paling dekat yaitu k=1 karena mengambil jarak tetangga yang paling dekat.
Seluruh percobaan yang telah dilakukan dapat disimpulkan bahwa hasil yang sempurna disebabkan oleh data yang sedikit dan sempit jangakuannya, yaitu hanya terdiri 50 organisme dengan variasi dari 5 genus yang berbeda. Jarak yang digunakan hanya kombinasi dari sebelah sekuens DNA-nya dengan jarak 1 dengan orientasi sudut 0°.
Saran
Beberapa saran untuk penelitian selanjutnya:
1 Menggunakan pendekatan GLCM memakai seluruh sudut yaitu 0°, 45°, 90°, 135°.
2 Menggunakan data dengan tingkatan takson yang mirip (satu genus satu ordo). 3 Menggunakan data lebih banyak.
13
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14
Lampiran 1 Daftar nama organisme
No Nama organisme No Nama organisme
1 Burkholderia ambifaria AMMD chromosome chromosome 1
26 Mycobacterium gilvum PYR-GCK chromosome 2 Burkholderia ambifaria MC40-6 chromosome chromosome 1 27 Mycobacterium leprae TN chromosome 3 Burkholderia cenocepacia AU 1054 chromosome 3 28 Mycobacterium marinum M 4 Burkholderia cenocepacia HI2424
chromosome chromosome 1 29 Mycobacterium smegmatis str. MC2 155 5 Burkholderia cenocepacia J2315 chromosome chromosome 1 30 Mycobacterium sp. JLS chromosome 6 Burkholderia cenocepacia MC0-3 chromosome chromosome 1 31 Staphylococcus aureus RF122 7 Burkholderia mallei ATCC 23344
chromosome chromosome 1
32 Staphylococcus aureus subsp. aureus COL chromosome
8 Burkholderia mallei NCTC 10229 chromosome I
33 Staphylococcus aureus subsp. aureus JH1
9 Burkholderia mallei NCTC 10247 chromosome I
34 Staphylococcus aureus subsp. aureus JH9
10 Burkholderia mallei SAVP1 chromosome I
35 Staphylococcus aureus subsp. aureus MRSA252 chromosome
11 Clostridium acetobutylicum ATCC 824 36 Staphylococcus aureus subsp. aureus MSSA476 chromosome
12 Clostridium beijerinckii NCIMB 8052 chromosome
37 Staphylococcus aureus subsp. aureus Mu3
13 Clostridium botulinum A3 str. Loch Maree
38 Staphylococcus aureus subsp. aureus Mu50
14 Clostridium botulinum A str. ATCC 19397
39 Staphylococcus aureus subsp. aureus MW2
15 Clostridium botulinum A str. ATCC 3502
40 Staphylococcus aureus subsp. aureus N315
16 Clostridium botulinum A str. Hall 41 Streptococcus agalactiae 2603V/R 17 Clostridium botulinum B1 str. Okra 42 Streptococcus agalactiae A909 18 Clostridium botulinum B str. Eklund
17B
43 Streptococcus agalactiae NEM316 19 Clostridium botulinum E3 str. Alaska
E43
44 Streptococcus equi subsp. zooepidemicus MGCS10565
20 Clostridium botulinum F str. Langeland 45 Streptococcus gordonii str. Challis substr. CH1
21 Mycobacterium abscessus chromosome 46 Streptococcus mutans UA159 chromosome
22 Mycobacterium avium 104 47 Streptococcus pneumoniae CGSP14 23 Mycobacterium avium subsp.
paratuberculosis K-10
48 Streptococcus pneumoniae D39 24 Mycobacterium bovis AF2122/97 49 Streptococcus pneumoniae G54 25 Mycobacterium bovis BCG str. Pasteur
1173P2
50 Streptococcus pneumoniae Hungary19A-6
15 Lampiran 2 Daftar nama genus
No Genus 1 Burkholderia 2 Clostridium 3 Mycobacterium 4 Staphylococcus 5 Streptococcus
16
Lampiran 3 Daftar nama data latih dan data uji Percobaan 1
Data latih
No Nama organisme No Nama organisme
1 Burkholderia cenocepacia AU 1054 chromosome 3
21 Mycobacterium leprae TN chromosome
2 Burkholderia cenocepacia HI2424 chromosome chromosome 1 22 Mycobacterium marinum M 3 Burkholderia cenocepacia J2315 chromosome chromosome 1 23 Mycobacterium smegmatis str. MC2 155 4 Burkholderia cenocepacia MC0-3 chromosome chromosome 1 24 Mycobacterium sp. JLS chromosome
5 Burkholderia mallei ATCC 23344 chromosome chromosome 1
25 Staphylococcus aureus subsp. aureus JH1
6 Burkholderia mallei NCTC 10229 chromosome I
26 Staphylococcus aureus subsp. aureus JH9
7 Burkholderia mallei NCTC 10247 chromosome I
27 Staphylococcus aureus subsp. aureus MRSA252 chromosome 8 Burkholderia mallei SAVP1
chromosome I
28 Staphylococcus aureus subsp. aureus MSSA476 chromosome 9 Clostridium botulinum A3 str. Loch
Maree
29 Staphylococcus aureus subsp. aureus Mu3
10 Clostridium botulinum A str. ATCC 19397
30 Staphylococcus aureus subsp. aureus Mu50
11 Clostridium botulinum A str. ATCC 3502
31 Staphylococcus aureus subsp. aureus MW2
12 Clostridium botulinum A str. Hall 32 Staphylococcus aureus subsp. aureus N315
13 Clostridium botulinum B1 str. Okra 33 Streptococcus agalactiae NEM316 14 Clostridium botulinum B str. Eklund
17B
34 Streptococcus equi subsp. zooepidemicus MGCS10565
15 Clostridium botulinum E3 str. Alaska E43
35 Streptococcus gordonii str. Challis substr. CH1
16 Clostridium botulinum F str. Langeland 36 Streptococcus mutans UA159 chromosome
17 Mycobacterium avium subsp. paratuberculosis K-10
37 Streptococcus pneumoniae CGSP14
18 Mycobacterium bovis AF2122/97 38 Streptococcus pneumoniae D39 19 Mycobacterium bovis BCG str. Pasteur
1173P2
39 Streptococcus pneumoniae G54 20 Mycobacterium gilvum PYR-GCK
chromosome
40 Streptococcus pneumoniae Hungary19A-6
Data Uji
No Nama organisme No Nama organisme
1 Burkholderia ambifaria AMMD chromosome chromosome 1
17 Lanjutan
No Nama organisme No Nama organisme
2 Burkholderia ambifaria MC40-6 chromosome chromosome 1
7 Staphylococcus aureus RF122
3 Clostridium acetobutylicum ATCC 824 8 Staphylococcus aureus subsp. aureus COL chromosome
4 Clostridium beijerinckii NCIMB 8052 chromosome
9 Streptococcus agalactiae 2603V/R 5 Mycobacterium abscessus chromosome 10 Streptococcus agalactiae A909
Percobaan 2 Data latih
No Nama organisme No Nama organisme
1 Burkholderia ambifaria AMMD chromosome chromosome 1 21 Mycobacterium leprae TN chromosome 2 Burkholderia ambifaria MC40-6 chromosome chromosome 1 22 Mycobacterium marinum M 3 Burkholderia cenocepacia J2315 chromosome chromosome 1 23 Mycobacterium smegmatis str. MC2 155 4 Burkholderia cenocepacia MC0-3 chromosome chromosome 1 24 Mycobacterium sp. JLS chromosome 5 Burkholderia mallei ATCC 23344
chromosome chromosome 1
25 Staphylococcus aureus RF122 6 Burkholderia mallei NCTC 10229
chromosome I
26 Staphylococcus aureus subsp. aureus COL chromosome
7 Burkholderia mallei NCTC 10247 chromosome I
27 Staphylococcus aureus subsp. aureus MRSA252 chromosome
8 Burkholderia mallei SAVP1 chromosome I
28 Staphylococcus aureus subsp. aureus MSSA476 chromosome
9 Clostridium acetobutylicum ATCC 824 29 Staphylococcus aureus subsp. aureus Mu3
10 Clostridium beijerinckii NCIMB 8052 chromosome
30 Staphylococcus aureus subsp. aureus Mu50
11 Clostridium botulinum A str. ATCC 3502
31 Staphylococcus aureus subsp. aureus MW2
12 Clostridium botulinum A str. Hall 32 Staphylococcus aureus subsp. aureus N315
13 Clostridium botulinum B1 str. Okra 33 Streptococcus agalactiae 2603V/R
14 Clostridium botulinum B str. Eklund 17B
34 Streptococcus agalactiae A909 15 Clostridium botulinum E3 str. Alaska
E43
35 Streptococcus gordonii str. Challis substr. CH1
16 Clostridium botulinum F str. Langeland 36 Streptococcus mutans UA159 chromosome
17 Mycobacterium abscessus chromosome 37 Streptococcus pneumoniae CGSP14 18 Mycobacterium avium 104 38 Streptococcus pneumoniae D39
18 Lanjutan
No Nama organisme No Nama organisme
19 Mycobacterium bovis BCG str. Pasteur 1173P2
39 Streptococcus pneumoniae G54 20 Mycobacterium gilvum PYR-GCK
chromosome
40 Streptococcus pneumoniae Hungary19A-6
Data uji
No Nama organisme No Nama organisme
1 Burkholderia cenocepacia AU 1054 chromosome 3
6 Mycobacterium bovis AF2122/97 2 Burkholderia cenocepacia HI2424
chromosome chromosome 1
7 Staphylococcus aureus subsp. aureus JH1
3 Clostridium botulinum A3 str. Loch Maree
8 Staphylococcus aureus subsp. aureus JH9
4 Clostridium botulinum A str. ATCC 19397
9 Streptococcus agalactiae NEM316 5 Mycobacterium avium subsp.
paratuberculosis K-10
10 Streptococcus equi subsp. zooepidemicus MGCS10565
Percobaan 3 Data latih
No Nama organisme No Nama organisme
1 Burkholderia ambifaria AMMD chromosome chromosome 1 21 Mycobacterium leprae TN chromosome 2 Burkholderia ambifaria MC40-6 chromosome chromosome 1 22 Mycobacterium marinum M 3 Burkholderia cenocepacia AU 1054 chromosome 3 23 Mycobacterium smegmatis str. MC2 155
4 Burkholderia cenocepacia HI2424 chromosome chromosome 1
24 Mycobacterium sp. JLS chromosome
5 Burkholderia mallei ATCC 23344 chromosome chromosome 1
25 Staphylococcus aureus RF122 6 Burkholderia mallei NCTC 10229
chromosome I
26 Staphylococcus aureus subsp. aureus COL chromosome
7 Burkholderia mallei NCTC 10247 chromosome I
27 Staphylococcus aureus subsp. aureus JH1
8 Burkholderia mallei SAVP1 chromosome I
28 Staphylococcus aureus subsp. aureus JH9
9 Clostridium acetobutylicum ATCC 824 29 Staphylococcus aureus subsp. aureus Mu3
10 Clostridium beijerinckii NCIMB 8052 chromosome
30 Staphylococcus aureus subsp. aureus Mu50
11 Clostridium botulinum A3 str. Loch Maree
31 Staphylococcus aureus subsp. aureus MW2
12 Clostridium botulinum A str. ATCC 19397
32 Staphylococcus aureus subsp. aureus N315
19 Lanjutan
No Nama organisme No Nama organisme
13 Clostridium botulinum B1 str. Okra 33 Streptococcus agalactiae 2603V/R 14 Clostridium botulinum B str. Eklund
17B
34 Streptococcus agalactiae A909 15 Clostridium botulinum E3 str. Alaska
E43
35 Streptococcus agalactiae NEM316 16 Clostridium botulinum F str. Langeland 36 Streptococcus equi subsp.
zooepidemicus MGCS10565
17 Mycobacterium abscessus chromosome 37 Streptococcus pneumoniae CGSP14 18 Mycobacterium avium 104 38 Streptococcus pneumoniae D39 19 Mycobacterium avium subsp.
paratuberculosis K-10
39 Streptococcus pneumoniae G54
20 Mycobacterium bovis AF2122/97 40 Streptococcus pneumoniae Hungary19A-6
Data uji
No Nama organisme No Nama organisme
1 Burkholderia cenocepacia J2315 chromosome chromosome 1
6 Mycobacterium gilvum PYR-GCK chromosome
2 Burkholderia cenocepacia MC0-3 chromosome chromosome 1
7 Staphylococcus aureus subsp. aureus MRSA252 chromosome
3 Clostridium botulinum A str. ATCC 3502
8 Staphylococcus aureus subsp. aureus MSSA476 chromosome
4 Clostridium botulinum A str. Hall 9 Streptococcus gordonii str. Challis substr. CH1
5 Mycobacterium bovis BCG str. Pasteur 1173P2
10 Streptococcus mutans UA159 chromosome
Percobaan 4 Data latih
No Nama organisme No Nama organisme
1 Burkholderia ambifaria AMMD chromosome chromosome 1
21 Mycobacterium bovis BCG str. Pasteur 1173P2
2 Burkholderia ambifaria MC40-6 chromosome chromosome 1
22 Mycobacterium gilvum PYR-GCK chromosome
3 Burkholderia cenocepacia AU 1054 chromosome 3
23 Mycobacterium smegmatis str. MC2 155
4 Burkholderia cenocepacia HI2424 chromosome chromosome 1 24 Mycobacterium sp. JLS chromosome 5 Burkholderia cenocepacia J2315 chromosome chromosome 1 25 Staphylococcus aureus RF122 6 Burkholderia cenocepacia MC0-3 chromosome chromosome 1
26 Staphylococcus aureus subsp. aureus COL chromosome
7 Burkholderia mallei NCTC 10247 chromosome I
27 Staphylococcus aureus subsp. aureus JH1
20 Lanjutan
No Nama organisme No Nama organisme
8 Burkholderia mallei SAVP1 chromosome I
28 Staphylococcus aureus subsp. aureus JH9
9 Clostridium acetobutylicum ATCC 824 29 Staphylococcus aureus subsp. aureus MRSA252 chromosome 10 Clostridium beijerinckii NCIMB 8052
chromosome
30 Staphylococcus aureus subsp. aureus MSSA476 chromosome 11 Clostridium botulinum A3 str. Loch
Maree
31 Staphylococcus aureus subsp. aureus MW2
12 Clostridium botulinum A str. ATCC 19397
32 Staphylococcus aureus subsp. aureus N315
13 Clostridium botulinum A str. ATCC 3502
33 Streptococcus agalactiae 2603V/R 14 Clostridium botulinum A str. Hall 34 Streptococcus agalactiae A909 15 Clostridium botulinum E3 str. Alaska
E43
35 Streptococcus agalactiae NEM316 16 Clostridium botulinum F str. Langeland 36 Streptococcus equi subsp.
zooepidemicus MGCS10565
17 Mycobacterium abscessus chromosome 37 Streptococcus gordonii str. Challis substr. CH1
18 Mycobacterium avium 104 38 Streptococcus mutans UA159 chromosome
19 Mycobacterium avium subsp. paratuberculosis K-10
39 Streptococcus pneumoniae G54 20 Mycobacterium bovis AF2122/97 40 Streptococcus pneumoniae
Hungary19A-6 Data uji
No Nama organisme No Nama organisme
1 Burkholderia mallei ATCC 23344 chromosome chromosome 1
6 Mycobacterium marinum M 2 Burkholderia mallei NCTC 10229
chromosome I
7 Staphylococcus aureus subsp. aureus Mu3
3 Clostridium botulinum B1 str. Okra 8 Staphylococcus aureus subsp. aureus Mu50
4 Clostridium botulinum B str. Eklund 17B
9 Streptococcus pneumoniae CGSP14
5 Mycobacterium leprae TN chromosome 10 Streptococcus pneumoniae D39 Percobaan 5
Data latih
No Nama organisme No Nama organisme
1 Burkholderia ambifaria AMMD chromosome chromosome 1
21 Mycobacterium bovis BCG str. Pasteur 1173P2
2 Burkholderia ambifaria MC40-6 chromosome chromosome 1
22 Mycobacterium gilvum PYR-GCK chromosome
21 Lanjutan
No Nama organisme No Nama organisme
3 Burkholderia cenocepacia AU 1054 chromosome 3
23 Mycobacterium leprae TN chromosome
4 Burkholderia cenocepacia HI2424 chromosome chromosome 1 24 Mycobacterium marinum M 5 Burkholderia cenocepacia J2315 chromosome chromosome 1 25 Staphylococcus aureus RF122 6 Burkholderia cenocepacia MC0-3 chromosome chromosome 1
26 Staphylococcus aureus subsp. aureus COL chromosome
7 Burkholderia mallei ATCC 23344 chromosome chromosome 1
27 Staphylococcus aureus subsp. aureus JH1
8 Burkholderia mallei NCTC 10229 chromosome I
28 Staphylococcus aureus subsp. aureus JH9
9 Clostridium acetobutylicum ATCC 824 29 Staphylococcus aureus subsp. aureus MRSA252 chromosome
10 Clostridium beijerinckii NCIMB 8052 chromosome
30 Staphylococcus aureus subsp. aureus MSSA476 chromosome
11 Clostridium botulinum A3 str. Loch Maree
31 Staphylococcus aureus subsp. aureus Mu3
12 Clostridium botulinum A str. ATCC 19397
32 Staphylococcus aureus subsp. aureus Mu50
13 Clostridium botulinum A str. ATCC 3502
33 Streptococcus agalactiae 2603V/R 14 Clostridium botulinum A str. Hall 34 Streptococcus agalactiae A909 15 Clostridium botulinum B1 str. Okra 35 Streptococcus agalactiae NEM316 16 Clostridium botulinum B str. Eklund
17B
36 Streptococcus equi subsp. zooepidemicus MGCS10565
17 Mycobacterium abscessus chromosome 37 Streptococcus gordonii str. Challis substr. CH1
18 Mycobacterium avium 104 38 Streptococcus mutans UA159 chromosome
19 Mycobacterium avium subsp. paratuberculosis K-10
39 Streptococcus pneumoniae CGSP14 20 Mycobacterium bovis AF2122/97 40 Streptococcus pneumoniae D39
Data uji
No Nama organisme No Nama organisme
1 Burkholderia mallei NCTC 10247 chromosome I
6 Mycobacterium sp. JLS chromosome 2 Burkholderia mallei SAVP1
chromosome I
7 Staphylococcus aureus subsp. aureus MW2
3 Clostridium botulinum E3 str. Alaska E43
8 Staphylococcus aureus subsp. aureus N315
4 Clostridium botulinum F str. Langeland 9 Streptococcus pneumoniae G54 5 Mycobacterium smegmatis str. MC2
155
10 Streptococcus pneumoniae Hungary19A-6
22
Lampiran 4 Daftar boxplot semua fitur dengan panjang 200 bp
Boxplot fitur Contrast
Boxplot fitur Correlation
23 Lanjutan
Boxplot fitur Inverse Different Moment
Boxplot fitur Entropy
24
Lanjutan
Boxplot fitur Sum Variance
Boxplot fitur Difference Variance
25 Lanjutan
Boxplot fitur Inverse Measures of Correlation 1
Boxplot fitur Inverse Measures of Correlation 2
26