Question: Pan and core genome analysis
0
gravatar for Sudhir Jadhao
5.4 years ago by
India
Sudhir Jadhao70 wrote:

Hello Everyone.

I have genome and predicted proteins of five Bacteria.

I want to know  two things from these data

1.how many genes are unique for particular bacteria

2.how many are unknown are unkonwn

eg.

Accession ID    Genome size     Orf no unknown orf nos  Unique orf no
Bacteria1 3796928    3485           ?                                    ?
Bacteria2 3960658    3646   ? ?
Bacteria3 3840286    3461 ? ?
Bacteria4 3936249    3590 ? ?
Bacteria5 3936249   4865 ? ?
         
         
         
         
         
         

 

pangenome bacteria • 1.6k views
ADD COMMENTlink modified 5.4 years ago by SES8.4k • written 5.4 years ago by Sudhir Jadhao70
0
gravatar for skbrimer
5.4 years ago by
skbrimer650
United States
skbrimer650 wrote:

You could try Spine and Agent out of the Hauser lab at northwestern. 

Ozer EA, Allen JP, and Hauser AR. Characterization of the core and accessory genomes of Pseudomonas aeruginosa using bioinformatic tools Spine and AGEnt. BMC Genomics 2014 15:737.

Spine gives you the core genome and agent gives you the accessory genome.  

ADD COMMENTlink written 5.4 years ago by skbrimer650

Thank you for kind reply,

I already tried Spine Agent but results are not  convincible

 

ADD REPLYlink written 5.4 years ago by Sudhir Jadhao70
0
gravatar for SES
5.4 years ago by
SES8.4k
Vancouver, BC
SES8.4k wrote:

There is a recently published tookit called Roary from the Sanger Pathogens group. It seems like it would be ideal for your study.

ADD COMMENTlink written 5.4 years ago by SES8.4k

Thank you for reply,

Roary takes GFF3 file as input

ADD REPLYlink written 5.4 years ago by Sudhir Jadhao70

Yes, it takes the (GFF3) output of Prokka. You did not mention anything about the input format. Was that a concern or just a comment?

ADD REPLYlink written 5.4 years ago by SES8.4k
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