Any Software To Do Multiple Genome Alignment For Bacterial Genomes?

Question

[sanchezcavani]

I need to do some staff on genome alignment of a few bacterial genomes to detect some conserved genes with synteny among them. However, since some of them have diverged for a long time (probably up to about 1 billion years), many software that are available may not work properly (mainly designed for plant and vertebrate genomes). Is there any suggestion? Thanks in advance!

[5heikki]

To what end? In my experience, genome alignments only work with closely related species.

[Josh Herr]

+1, I agree that there needs to be a purpose. You're right in that alignments need homologous regions, but I would argue that most bacteria have some homologous regions that may be aligned. This still does not make genome alignment a valuable or meaningful exercise unless a research focus or question is present.

Answer 1

[Josh Herr]

This question gets asked quite frequently around here -- see these answers for more information:

Help With Multiple Whole Genome Alignment. Aligning Over 400 Whole Genomes

Whole Genome Phylogeny

How To Do Multiple Whole Genomes Alignments?

Pairwise Genome Alignment

Phylogenetic Analysis Of Whole Genomes

I would disagree with you that the software works preferentially for Eukaryotes over Bacteria or Archaea. I have used the same synteny tools on plants, fungi, and bacteria (some viruses too) with similar results. I would recommend Mauve and Symap for synteny anaysis, BRIG for bacterial synteny analysis and visualization, and Circos for visualization, but there are many other tools out there to choose from.

[sanchezcavani]

Thanks so much for your helpful suggestions for many nice resources!

Answer 2

[GouthamAtla]

SyMap would do that. It will give Synteny views. It runs BLAT, MuMMER and NCUMER internally to peform alignment.

[sanchezcavani]

Thanks for your suggestions. SyMap seems to be a good aligner.