Comparative Bacterial genome alignments

Question

[glady]

Hello friends, I have some bacterial draft genomes and they belong to different ecological niches. I want to do a comparative study, from which I can predict if there are any functions which are similar in all of them even after coming from different ecological backgrounds. And which genes or compounds are responsible for the functions. Can you help in constructing a pipeline for this doing this work? Till now, I am thinking of;

1) predicting the common orthologus groups with **OrthoMCL**
2) predicting the common SNP's
3) determing the COG's
4) genome visualization by CIRCOS
5) phylogeny analysis

[Naren]

BPGA can be used for your task except genome visualization and SNP.

[glady]

The analysis asked by me in the above question, is that much analysis enough for achieving my goal of performing comparative study or is there a need for me to do some further analysis? If yes, then please suggest those improvisation. Thank you for your reply

[GenoMax]

If the genomes are related then for the genome comparison part give Mauve a try.

Answer 1

[Naren]

Comparing KEGG (Metabolic Pathway) and COG (Function analysis) profiles of the organisms will help. Pan genome analysis will help to find common gene functions and species specific gene functions and their role in metabolism. Try running full analysis with BPGA pipeline or any suitable tool. This may help you to think your own pipeline concept. Refer to BPGA Article in Scientific Reports.

[glady]

Thank you sir, BPGA has really helped a lot. How can we look for some environment specific genes in our genomes ?

[Naren]

Yeah try subset analysis and create groups according to environment. Refer to detailed documentation of BPGA. Also refer to BPGA Userguide for subset/grouping analysis.