Comparing bacterial genomes

[Adham]

Hi everybody,
I am beginner in the field of bacterial genomics and bioinformatics, and I have 8 de novo assembled bacterial genomes and 2 ref. genomes from NCBI. I would like compare all the 10 genomes against each other to to detect the unique sequence fragments (or genes) that are present only in my genomes, also the similarities to the ref. genomes.

I hope that someone could help me with suggestions on how I could do so and which tool(s) or scripts are available for this purpose.


Thank you so much in advance

[GenoMax]

Try Mauve: http://darlinglab.org/mauve/mauve.html

[yzzhang]

If you want to focus on genes, you can try blast methods such as bidirectional best hit, OMCL, etc. several software can do this. I used Get_homologues and it worked well.

[Adham]

GenoMax and yzzhang, Thank you so much for your prompt reply.
Indeed, I was algined my genomes using Mauve, but I could only check it manually.
Is there a way to export the differences as fasta file or table with start and end positions?

Thank you so much

[GenoMax]

Different kinds of files mauve produces: http://darlinglab.org/mauve/user-guide/files.html