Pan and core genome analysis

Question

[Sudhir Jadhao]

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 unknown

e.g.,

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            ?                 ?

Answer 1

[skbrimer]

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.

[Sudhir Jadhao]

Thank you for kind reply,

I already tried Spine Agent but results are not convincing

Answer 2

[SES]

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

[Sudhir Jadhao]

Thank you for reply,

Roary takes GFF3 file as input

[SES]

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?