fnec Gene Table Build 14_03_11 [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) BL
2) DJ-1
3) BFTR-1
4) DAB
5) BFTR-2
6) DJ-2
7) D12
8) ATCC51357
9) Fnf1007
Show genes only present in
1) BL
2) DJ-1
3) BFTR-1
4) DAB
5) BFTR-2
6) DJ-2
7) D12
8) ATCC51357
9) Fnf1007
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Show genes not present in
1) BL
2) DJ-1
3) BFTR-1
4) DAB
5) BFTR-2
6) DJ-2
7) D12
8) ATCC51357
9) Fnf1007


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

Fusobacterium necrophorum BL

Fusobacterium necrophorum DJ-1

Fusobacterium necrophorum BFTR-1

Fusobacterium necrophorum DAB

Fusobacterium necrophorum BFTR-2

Fusobacterium necrophorum DJ-2

Fusobacterium necrophorum D12

Fusobacterium necrophorum subsp. funduliforme ATCC

Fusobacterium necrophorum subsp. funduliforme Fnf

1p-cluster009383 Uncategoriziedhypothetical protein627* * * *          
2p-cluster016128 Uncategoriziedhypothetical protein426            *    
3rrna-cluster000001 Uncategorizied16S ribosomal RNA1510* * * * * * * * *
4p-cluster000133 COG0532 [J]translation initiation factor IF-22139  * *            
5p-cluster000134 COG0858 [J]ribosome-binding factor A369                 
6p-cluster001692 COG0608 [L]single-stranded DNA exonuclease Rec2529        *        
7p-cluster000136 COG0544 [O]trigger factor1290  *     *        
8p-cluster000137 COG0740 [OU]ATP-dependent Clp protease proteoly588                 
9p-cluster000138 COG1219 [O]Clp protease ATP-binding protein1293                 
10p-cluster003360 COG0466 [O]Lon protease2328      *          
11p-cluster007213 COG0466 [O]hypothetical protein478      *          
12p-cluster000140 COG0218 [R]GTP-binding protein YsxC615                 
13p-cluster000141 COG0060 [J]valyl-tRNA synthase2664                 
14p-cluster000142 COG0583 [K]LysR family transcriptional regulat873                 
15p-cluster000143 COG0279 [G]phosphoheptose isomerase582                 
16p-cluster002637 COG5266 [P]ABC transporter substrate-binding p945  *             *
17p-cluster016826 COG1629 [P]TonB-dependent receptor plug domain2256  *              
18p-cluster016825 Uncategoriziedhypothetical protein213  *              
19p-cluster003352 Uncategoriziedhypothetical protein183  *              
20p-cluster000148 Uncategoriziedhypothetical protein168                 
21p-cluster000149 Uncategoriziedtoxin RelE267  *              
22p-cluster012539 Uncategoriziedhypothetical protein372    *            
23p-cluster001869 COG1136 [V]ABC transporter825                 
24p-cluster001870 COG0378 [OK]hypothetical protein693                 
25p-cluster001871 COG1840 [P]spermidine/putrescine ABC transport1200                 
26p-cluster001872 Uncategoriziedhypothetical protein225        *        
27p-cluster001873 COG1974 [KT]peptidase S24645        *        
28p-cluster001874 COG0384 [R]phenazine biosynthesis protein PhzF864                 
29p-cluster001875 COG4912 [L]DNA alkylation repair enzyme699          *      
30p-cluster002645 Uncategoriziedhypothetical protein339          *      
31p-cluster002646 COG3600 [S]hypothetical protein441                 
32p-cluster002647 Uncategoriziedhypothetical protein822                 
33p-cluster002648 COG1961 [L]resolvase1425        *        
34p-cluster002649 Uncategoriziedhypothetical protein186                 
35p-cluster000846 Uncategoriziedhypothetical protein516        *        
36p-cluster002651 Uncategoriziedhypothetical protein276                 
37p-cluster017528 Uncategoriziedhypothetical protein342        *   *    
38p-cluster002653 Uncategoriziedhypothetical protein96                 
39p-cluster020000 Uncategoriziedhypothetical protein681        *        
40p-cluster017771 COG1192 [D]CobQ/CobB/MinD/ParA nucleotide bind1083        *       *
41p-cluster011347 Uncategoriziedhypothetical protein280        *        
42p-cluster011346 Uncategoriziedhypothetical protein213        *       *
43p-cluster002657 Uncategoriziedhypothetical protein1017        *        
44p-cluster002658 Uncategoriziedhypothetical protein228        *        
45p-cluster009576 Uncategoriziedhypothetical protein297                 
46p-cluster002660 Uncategoriziedhypothetical protein96                 
47p-cluster002661 Uncategoriziedhypothetical protein237                 
48p-cluster011290 Uncategoriziedtranscriptional regulator234        *       *
49p-cluster020350 Uncategoriziedputative lipoprotein744  *             *
50p-cluster020352 Uncategoriziedhypothetical protein243                 

Please send any comment/suggestion to kitticho@uw.edu
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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