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

Keyword search
Search for
Also include clusters with significant sequence similarity
Also include clusters containing upstream and downstream genes (Must sort rows by Gene position in a genome first)

BLAST search
Sequence type

Row sorting and cell coloring options
Sort rows by Order rows in
Color cells by Display rows

Row filtering options
 Show COG of type
 Show clusters with minimum expected length of bp
Show clusters containing genes near the ends of contigs
Show clusters containing genes with frameshift mutation

Display column
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
All genomes (Core genes)
Some genomes (Variable genes)

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


<< Prev    Next >>
First Page    Last Page
Go to page   / 63  

# 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

1trna-cluster000191 UncategoriziedtRNA-Ile77            *    
2trna-cluster000125 UncategoriziedtRNA-Asn76        *   *    
3trna-cluster000051 UncategoriziedtRNA-Lys76  * * *       * *
4trna-cluster000039 UncategoriziedtRNA-Ser85                 
5trna-cluster000038 UncategoriziedtRNA-Thr76              *  
6trna-cluster000035 UncategoriziedtRNA-Arg77                 
7trna-cluster000034 UncategoriziedtRNA-Arg77                 
8trna-cluster000033 UncategoriziedtRNA-Ser85*         *   *  
9trna-cluster000029 UncategoriziedtRNA-Met77*   *         * *
10trna-cluster000028 UncategoriziedtRNA-Arg77*   *         * *
11trna-cluster000026 UncategoriziedtRNA-Val76*         *      
12trna-cluster000024 UncategoriziedtRNA-Phe76*         *   * *
13trna-cluster000023 UncategoriziedtRNA-Cys74  * * * * *   * *
14trna-cluster000022 UncategoriziedtRNA-Thr76      *       * *
15trna-cluster000021 UncategoriziedtRNA-Glu75* * *   * *   * *
16trna-cluster000020 UncategoriziedtRNA-Tyr85* *     * * * *  
17trna-cluster000019 UncategoriziedtRNA-Asp78*   * *          
18trna-cluster000018 UncategoriziedtRNA-Met77* * * * *     *  
19trna-cluster000017 UncategoriziedtRNA-Leu88* * * * *     *  
20trna-cluster000016 UncategoriziedtRNA-Leu84  *   * *     *  
21trna-cluster000015 UncategoriziedtRNA-Lys76*   *         * *
22trna-cluster000014 UncategoriziedtRNA-His76              *  
23trna-cluster000012 UncategoriziedtRNA-Pro77*   * *     * * *
24trna-cluster000011 UncategoriziedtRNA-Gln75* * * * * * *   *
25trna-cluster000010 UncategoriziedtRNA-Trp76                 
26trna-cluster000009 UncategoriziedtRNA-Gly76  * * *       * *
27trna-cluster000008 UncategoriziedtRNA-Ala77            *    
28trna-cluster000007 UncategoriziedtRNA-Met77        *        
29trna-cluster000006 UncategoriziedtRNA-Leu87  * * *   *      
30trna-cluster000005 UncategoriziedtRNA-Ser85        *        
31trna-cluster000004 UncategoriziedtRNA-Ser90      * *       *
32trna-cluster000002 UncategoriziedtRNA-Thr76* * * * * *   * *
33trna-cluster000001 UncategoriziedtRNA-Arg77            *   *
34rrna-cluster000036 Uncategorizied23S ribosomal RNA2913* * * * * *   * *
35rrna-cluster000023 Uncategorizied23S ribosomal RNA112          *      
36rrna-cluster000007 Uncategorizied5S ribosomal RNA117* * *   * * * * *
37rrna-cluster000001 Uncategorizied16S ribosomal RNA1510* * * * * * * * *
38p-cluster020423 Uncategoriziedhypothetical protein272                *
39p-cluster020415 Uncategoriziedputative AAA-ATPase759*   *   * *     *
40p-cluster020407 COG1396 [K]DNA-binding helix-turn-helix protei369                *
41p-cluster020406 COG3177 [S]Fic/DOC family protein1164                 
42p-cluster020405 Uncategoriziedhypothetical protein156                 
43p-cluster020404 COG2932 [K]peptidase S24-like protein714                *
44p-cluster020390 Uncategoriziedhypothetical protein3024      *     *   *
45p-cluster020352 Uncategoriziedhypothetical protein243                 
46p-cluster020351 Uncategoriziedhypothetical protein276                 
47p-cluster020350 Uncategoriziedputative lipoprotein744  *             *
48p-cluster020345 Uncategoriziedhypothetical protein135                *
49p-cluster020344 Uncategoriziedphage replisome organizer N-termina849                 
50p-cluster020337 Uncategoriziedhypothetical protein116                *

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

tumblr site counter

 

Gene Completeness

>=100%
=70%
<70%

: Similar sequence present
: Not present

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