fnuc Gene Table Build 14_03_12 [A quick tutorial]

Citation
Kittichotirat W, Bumgarner RE, Asikainen S, Chen C, 2011
Identification of the Pangenome and Its Components in 14 Distinct Aggregatibacter actinomycetemcomitans Strains by Comparative Genomic Analysis
PLoS ONE 6(7): e22420. doi:10.1371/journal.pone.0022420

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1) YH7053
2) YH7054
3) YH7055
4) YH7056
5) YH7199
6) animalis-4_8
7) animalis-3_1_33
8) animalis-7_1
9) animalis-D11
10) animalis-ATCC51191
11) animalis-F0419
12) animalis-21_1A
13) animalis-11_3_2
14) fusiforme-ATCC51190
15) nucleatum-ATCC23726
16) polymorphum-ATCC10953
17) polymorphum-F0401
18) vincentii-3_1_36A2
19) vincentii-4_1_13
20) 13_3C
21) CTI-5
22) CTI-6
23) CTI-7
Show genes only present in
1) YH7053
2) YH7054
3) YH7055
4) YH7056
5) YH7199
6) animalis-4_8
7) animalis-3_1_33
8) animalis-7_1
9) animalis-D11
10) animalis-ATCC51191
11) animalis-F0419
12) animalis-21_1A
13) animalis-11_3_2
14) fusiforme-ATCC51190
15) nucleatum-ATCC23726
16) polymorphum-ATCC10953
17) polymorphum-F0401
18) vincentii-3_1_36A2
19) vincentii-4_1_13
20) 13_3C
21) CTI-5
22) CTI-6
23) CTI-7
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Some genomes (Variable genes)

Show genes not present in
1) YH7053
2) YH7054
3) YH7055
4) YH7056
5) YH7199
6) animalis-4_8
7) animalis-3_1_33
8) animalis-7_1
9) animalis-D11
10) animalis-ATCC51191
11) animalis-F0419
12) animalis-21_1A
13) animalis-11_3_2
14) fusiforme-ATCC51190
15) nucleatum-ATCC23726
16) polymorphum-ATCC10953
17) polymorphum-F0401
18) vincentii-3_1_36A2
19) vincentii-4_1_13
20) 13_3C
21) CTI-5
22) CTI-6
23) CTI-7


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# Cluster ID COG Function Annotation Expected gene Length (bp)

Fusobacterium nucleatum YH7053

Fusobacterium nucleatum YH7054

Fusobacterium nucleatum YH7055

Fusobacterium nucleatum YH7056

Fusobacterium nucleatum YH7199

Fusobacterium nucleatum subsp. animalis 4_8

Fusobacterium nucleatum subsp. animalis 3_1_33

Fusobacterium nucleatum subsp. animalis 7_1

Fusobacterium nucleatum subsp. animalis D11

Fusobacterium nucleatum subsp. animalis ATCC 51191

Fusobacterium nucleatum subsp. animalis F0419

Fusobacterium nucleatum subsp. animalis 21_1A

Fusobacterium nucleatum subsp. animalis 11_3_2

Fusobacterium nucleatum subsp. fusiforme ATCC 5119

Fusobacterium nucleatum subsp. nucleatum ATCC 2372

Fusobacterium nucleatum subsp. polymorphum ATCC 10

Fusobacterium nucleatum subsp. polymorphum F0401

Fusobacterium nucleatum subsp. vincentii 3_1_36A2

Fusobacterium nucleatum subsp. vincentii 4_1_13

Fusobacterium nucleatum 13_3C

Fusobacterium nucleatum CTI-5

Fusobacterium nucleatum CTI-6

Fusobacterium nucleatum CTI-7

1p-cluster000473 Uncategoriziedchromosomal replication initiator p1914* * * * * *       *       *     * *          
2p-cluster000472 COG2501 [S]RNA-binding protein S4216                                *            
3p-cluster000471 COG1195 [L]recombinase RecF1110                  *             *            
4p-cluster000470 Uncategoriziedhypothetical protein273                  *                          
5p-cluster016908 COG0187 [L]DNA topoisomerase (ATP-hydrolyzing)1920                  *                          
6p-cluster032866 Uncategoriziedhypothetical protein180                                             
7p-cluster000468 COG0188 [L]DNA gyrase subunit A2436                                             
8p-cluster000467 COG0622 [R]phosphodiesterase462                                             
9p-cluster039716 COG0016 [J]phenylalanyl-tRNA synthetase alpha 1038                                             
10p-cluster000465 COG0072 [J]phenylalanyl-tRNA synthetase subuni2397                  *                          
11p-cluster019612 COG0072 [J]phenylalanyl-tRNA synthetase subuni339                  *                          
12p-cluster026639 COG2849 [S]hypothetical protein1821    * *           *         *           *    
13p-cluster026639 COG2849 [S]hypothetical protein1821    * *           *         *           *    
14p-cluster026639 COG2849 [S]hypothetical protein1821    * *           *         *           *    
15p-cluster040015 COG2849 [S]hypothetical protein312                                             
16p-cluster026639 COG2849 [S]hypothetical protein1821    * *           *         *           *    
17p-cluster029643 COG2849 [S]hypothetical protein156                                             
18p-cluster014780 Uncategoriziedhypothetical protein123                                             
19p-cluster016115 Uncategoriziedhypothetical protein120                                             
20p-cluster001050 COG1943 [L]transposase459  * * * *         *     * *         *        
21p-cluster024296 COG1943 [L]hypothetical protein195                                             
22p-cluster049525 Uncategoriziedhypothetical protein94                                            *
23p-cluster000461 COG0451 [MG]UDP-glucose 4-epimerase990                                             
24p-cluster000460 COG4468 [G]galactose-1-phosphate uridylyltrans1530                                             
25p-cluster019618 COG0153 [G]galactokinase1221                  *                          
26p-cluster018246 COG1288 [S]C4-dicarboxylate anaerobic carrier1581* *   *           *       *                 *
27p-cluster049533 COG3333 [S]hypothetical protein1491                                             
28p-cluster000455 COG3333 [S]hypothetical protein462* *   * *                                    
29p-cluster018251 Uncategoriziedhypothetical protein447* *   *                                      
30p-cluster023767 COG3181 [S]hypothetical protein978                                             
31p-cluster035455 COG0488 [R]ABC transporter ATP-binding protein1902                * *                          
32p-cluster001066 COG0697 [GER]membrane protein906                                             
33p-cluster014718 COG1404 [O]hypothetical protein2337                  *                          
34p-cluster019629 COG2832 [S]hypothetical protein438                                             
35p-cluster019630 COG0489 [D]Mrp ATPase family protein783    *                                        
36p-cluster016886 Uncategoriziedhypothetical protein612        *         *                          
37p-cluster016885 Uncategoriziedhypothetical protein198        *                                    
38p-cluster020415 Uncategoriziedhypothetical protein261                                             
39p-cluster028877 Uncategoriziedhypothetical protein213                                             
40p-cluster034304 Uncategoriziedhypothetical protein90                                             
41p-cluster001072 COG2804 [NU]general secretion pathway protein G1245    *   *                                    
42p-cluster001073 COG1459 [NU]general secretion pathway protein G1041                                             
43p-cluster001074 COG2165 [NU]general secretion pathway protein G489                  *                          
44p-cluster029975 Uncategoriziedhypothetical protein501    *                                        
45p-cluster020478 Uncategoriziedhypothetical protein171                                             
46p-cluster027807 Uncategoriziedhypothetical protein216                                             
47p-cluster001075 Uncategoriziedhypothetical protein414    *             *                          
48p-cluster042064 Uncategoriziedprepilin-type cleavage/methylation 579                                             
49p-cluster001076 Uncategoriziedhypothetical protein558                                             
50p-cluster008626 Uncategoriziedfimbrial assembly protein1179                  *                          

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Gene Completeness

>=100%
=70%
<70%

: Similar sequence present
: Not present

* : Within 300 bp from ends
F : Possible frameshift
I : Island genes