Question: Any Software To Do Multiple Genome Alignment For Bacterial Genomes?
3
gravatar for sanchezcavani
5.2 years ago by
sanchezcavani210
Canada
sanchezcavani210 wrote:

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!

bacteria alignment • 7.4k views
ADD COMMENTlink modified 5.1 years ago by Josh Herr5.6k • written 5.2 years ago by sanchezcavani210
1

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

ADD REPLYlink written 5.2 years ago by 5heikki8.3k

+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.

ADD REPLYlink modified 5.2 years ago • written 5.2 years ago by Josh Herr5.6k
6
gravatar for Josh Herr
5.2 years ago by
Josh Herr5.6k
University of Nebraska
Josh Herr5.6k wrote:

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.

ADD COMMENTlink modified 5.1 years ago • written 5.2 years ago by Josh Herr5.6k

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

ADD REPLYlink written 5.1 years ago by sanchezcavani210
1
gravatar for geek_y
5.1 years ago by
geek_y9.3k
Barcelona/CRG/London/Imperial
geek_y9.3k wrote:

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

ADD COMMENTlink written 5.1 years ago by geek_y9.3k

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

ADD REPLYlink written 5.1 years ago by sanchezcavani210
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