aa_ha Gene Table Build 14_10_01 [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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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)

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 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

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1) D17P-3new
2) D7S-1new
3) H5P-1new
4) I63Bnew
5) SA508
6) SA3733
7) SA3033
8) SA269
9) SA2200
10) D18P-1new
11) SC29R
12) SA2876
13) SCC393new
14) A160new
15) SC936
16) SC1083
17) SA3096
18) ANH9776
19) RHAAInew
20) HK1651new
21) ANH9381gb
22) SCC1398new
23) SCC4092new
24) I23Cnew
25) S23Anew
26) D11S-1new
27) D17P-2new
28) SA2149
29) SC383s
30) SCC2302new
31) AAS4anew
32) ATCC33389new
33) NJ8700new
Show genes only present in
1) D17P-3new
2) D7S-1new
3) H5P-1new
4) I63Bnew
5) SA508
6) SA3733
7) SA3033
8) SA269
9) SA2200
10) D18P-1new
11) SC29R
12) SA2876
13) SCC393new
14) A160new
15) SC936
16) SC1083
17) SA3096
18) ANH9776
19) RHAAInew
20) HK1651new
21) ANH9381gb
22) SCC1398new
23) SCC4092new
24) I23Cnew
25) S23Anew
26) D11S-1new
27) D17P-2new
28) SA2149
29) SC383s
30) SCC2302new
31) AAS4anew
32) ATCC33389new
33) NJ8700new
All genomes (Core genes)
Some genomes (Variable genes)

Show genes not present in
1) D17P-3new
2) D7S-1new
3) H5P-1new
4) I63Bnew
5) SA508
6) SA3733
7) SA3033
8) SA269
9) SA2200
10) D18P-1new
11) SC29R
12) SA2876
13) SCC393new
14) A160new
15) SC936
16) SC1083
17) SA3096
18) ANH9776
19) RHAAInew
20) HK1651new
21) ANH9381gb
22) SCC1398new
23) SCC4092new
24) I23Cnew
25) S23Anew
26) D11S-1new
27) D17P-2new
28) SA2149
29) SC383s
30) SCC2302new
31) AAS4anew
32) ATCC33389new
33) NJ8700new


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

Serotype-a D17P3 New

Serotype-a D7S-1 New

Serotype-a H5P1 New

Serotype-d I63B New

Serotype-d SA508

Serotype-d SA3733

Serotype-d SA3033

Serotype-d SA269

Serotype-d SA2200

Serotype-f D18P1 New

Serotype-f SC29R

Serotype-e SA2876

Serotype-e SCC393 New

Serotype-e A160 New

Serotype-e SC936

Serotype-e SC1083

Serotype-e SA3096

Serotype-e ANH9776

Serotype-b RHAA1 New

Serotype-b HK1651 New

Serotype-b ANH9381 Genbank

Serotype-b SCC1398 New

Serotype-b SCC4092 New

Serotype-b I23C New

Serotype-b S23A New

Serotype-c D11S-1 New

Serotype-c D17P2 New

Serotype-c SA2149

Serotype-c SC383s

Serotype-c SCC2302 New

Serotype-c AAS4A New

ATCC33389 New

NJ8700 New

1p-cluster01091 COG0633 [C](2Fe-2S)-binding protein288        * *                       *                              
2p-cluster00197 COG0621 [J](dimethylallyl)adenosine tRNA methy1422        * *     *     *           *                              
3p-cluster00054 COG0317 [TK](p)ppGpp synthetase2229      * * *                       *                              
4p-cluster01813 COG2357 [S](p)ppGpp synthetase996                    *                                            
5p-cluster00485 COG1575 [H]1,4-dihydroxy-2-naphthoate prenyltr942        *                         *                              
6p-cluster06199 COG0106 [E]1-(5-phosphoribosyl)-5-[(5- phospho552                                                                 
7p-cluster02605 COG0204 [I]1-acyl-sn-glycerol-3-phosphate acyl807        * *   *                   *                              
8p-cluster14730 COG0204 [I]1-acyl-sn-glycerol-3-phosphate acyl216                *                                                
9p-cluster00271 COG0743 [I]1-deoxy-D-xylulose 5-phosphate redu1281          * *   *         *     *                                
10p-cluster00092 COG1154 [HI]1-deoxy-D-xylulose-5-phosphate synt1857        * *     * *             * *                              
11p-cluster00487 COG1105 [G]1-phosphofructokinase939                                                                 
12rrna-cluster00003 Uncategorizied16S ribosomal RNA1610*   * * * * * * * * * * * * * * * *       * * * *   * * * * * *  
13rrna-cluster00009 Uncategorizied16S ribosomal RNA52                                          *                      
14rrna-cluster00010 Uncategorizied16S ribosomal RNA247                    *                                            
15p-cluster00460 COG0275 [M]16S rRNA methyltransferase966          *                       *                              
16p-cluster00691 COG1385 [S]16S rRNA methyltransferase732          *                                                      
17p-cluster01382 COG0742 [L]16S rRNA methyltransferase594          *                                                      
18p-cluster00736 COG0357 [M]16S rRNA methyltransferase GidB642        * *   *                   *                              
19p-cluster00881 COG0806 [J]16S rRNA-processing protein RimM525                                                                 
20p-cluster01140 COG0737 [F]2, 3-cyclic nucleotide 2-phosphodie1974      * *                                                        
21p-cluster01195 COG0617 [J]2, 3-cyclic nucleotide 2-phosphodie1302                                                                 
22p-cluster00592 COG2171 [E]2,3,4,5-tetrahydropyridine-2,6-carb825                                  *                              
23p-cluster07260 COG0656 [R]2,5-diketo-D-gluconic acid reductas960                                                                 
24p-cluster01181 COG1767 [H]2-(5-triphosphoribosyl)-3-dephospho1410          *                                                      
25p-cluster01119 COG0318 [IQ]2-acyl-glycerophospho-ethanolamine 3459        * *   * *     *           *                              
26p-cluster01568 COG0245 [I]2-C-methyl-D-erythritol 2,4-cyclodi477                                                                 
27p-cluster01348 COG1211 [I]2-C-methyl-D-erythritol 4-phosphate693