Thanks so much for your helpful suggestions for many nice resources!
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Any Software To Do Multiple Genome Alignment For Bacterial Genomes?
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!
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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
How To Do Multiple Whole Genomes Alignments?
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.
SyMap would do that. It will give Synteny views. It runs BLAT, MuMMER and NCUMER internally to peform alignment.
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GouthamAtla
Thanks for your suggestions. SyMap seems to be a good aligner.
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To what end? In my experience, genome alignments only work with closely related species.
+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.