hpar 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) HPS-ST41
2) HPS-ST42
3) HPS9
4) HPS10
5) HPS11
Show genes only present in
1) HPS-ST41
2) HPS-ST42
3) HPS9
4) HPS10
5) HPS11
All genomes (Core genes)
Some genomes (Variable genes)

Show genes not present in
1) HPS-ST41
2) HPS-ST42
3) HPS9
4) HPS10
5) HPS11


<< Prev    Next >>
First Page    Last Page
Go to page   / 48  

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

Haemophilus parasuis ST4-1

Haemophilus parasuis ST4-2

Haemophilus parasuis HPS9

Haemophilus parasuis HPS10

Haemophilus parasuis HPS11

1trna-cluster000161 UncategoriziedtRNA-Trp74         
2trna-cluster000149 UncategoriziedtRNA-Leu85         
3trna-cluster000135 UncategoriziedtRNA-Glu76    * * *
4trna-cluster000093 UncategoriziedtRNA-Ile77  * * * *
5trna-cluster000092 UncategoriziedtRNA-Ala76  * * * *
6trna-cluster000090 UncategoriziedtRNA-Asn76         
7trna-cluster000047 UncategoriziedtRNA-Met77         
8trna-cluster000045 UncategoriziedtRNA-Ser90      * *
9trna-cluster000044 UncategoriziedtRNA-Val77         
10trna-cluster000042 UncategoriziedtRNA-Ala76         
11trna-cluster000039 UncategoriziedtRNA-Val76*       *
12trna-cluster000038 UncategoriziedtRNA-Ser95         
13trna-cluster000036 UncategoriziedtRNA-Arg77         
14trna-cluster000034 UncategoriziedtRNA-Arg77*     * *
15trna-cluster000033 UncategoriziedtRNA-His76*   * * *
16trna-cluster000029 UncategoriziedtRNA-Lys76         
17trna-cluster000028 UncategoriziedtRNA-Met77        *
18trna-cluster000027 UncategoriziedtRNA-Leu85        *
19trna-cluster000025 UncategoriziedtRNA-Gln75        *
20trna-cluster000024 UncategoriziedtRNA-Arg77         
21trna-cluster000023 UncategoriziedtRNA-Pro77* * * * *
22trna-cluster000022 UncategoriziedtRNA-Leu86         
23trna-cluster000020 UncategoriziedtRNA-Asn76    *    
24trna-cluster000019 UncategoriziedtRNA-Phe76    *    
25trna-cluster000015 UncategoriziedtRNA-Asp77* * * *  
26trna-cluster000014 UncategoriziedtRNA-Trp76* *     *
27trna-cluster000013 UncategoriziedtRNA-Sec95         
28trna-cluster000012 UncategoriziedtRNA-Ser90         
29trna-cluster000011 UncategoriziedtRNA-Thr76* * * * *
30trna-cluster000010 UncategoriziedtRNA-Gly75         
31trna-cluster000009 UncategoriziedtRNA-Tyr85         
32trna-cluster000008 UncategoriziedtRNA-Thr76      * *
33trna-cluster000006 UncategoriziedtRNA-Leu87      * *
34trna-cluster000005 UncategoriziedtRNA-Met77         
35trna-cluster000004 UncategoriziedtRNA-Leu86         
36trna-cluster000003 UncategoriziedtRNA-Gly76  *   * *
37trna-cluster000002 UncategoriziedtRNA-Cys74        *
38trna-cluster000001 UncategoriziedtRNA-Arg77* *      
39rrna-cluster000021 Uncategorizied23S ribosomal RNA3032* * * * *
40rrna-cluster000020 Uncategorizied16S ribosomal RNA1542* * * * *
41rrna-cluster000016 Uncategorizied16S ribosomal RNA71    *    
42rrna-cluster000009 Uncategorizied16S ribosomal RNA436  * *    
43rrna-cluster000005 Uncategorizied5S ribosomal RNA116* * * *  
44rrna-cluster000004 Uncategorizied23S ribosomal RNA338*        
45p-cluster010099 Uncategoriziedhypothetical protein883        *
46p-cluster010083 COG3203 [M]membrane protein1191         
47p-cluster010017 Uncategoriziedhypothetical protein180         
48p-cluster010007 Uncategoriziedhypothetical protein245        *
49p-cluster009997 Uncategoriziedhypothetical protein636      * *
50p-cluster009996 Uncategoriziedhypothetical protein324         

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