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Mauve tool, Genome alignment
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3.4 years ago
Nitha • 10

Hi All,

I am trying to look genome alignment for my bacteria genome with my reference genome. From literature I came to know about Mauve tool. I am not able to understand fully to handle this tools, I have some doubts regarding this tool.

  1. Can I use CDS (fasta or Genebank full format) as input for tooll, its possible to check the alignment? Whether only contigs are used for checking genome alignment??

  2. My bacteria, consist of Plasmid so, I get 2files. one is CDS and Plasmid, can I do do separately alignment for these two sequence or combined? And if I take gene bank format, I feel that I am making mistake in concatenated two files.. so I used to fasta files to concatenated (CDS and Plasmid).

  3. I have used reference genome in genbank format (.gb). or whether I have to use .fna file.

  4. I am trying to run Mauve in windows platform with 64 bits.

Can anyone guide me, to use Mauve...


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1) Probably the full genbank file if your best bet; just a fasta of the CDSs lack the context for the alignment. 2) It can handle multiple contigs if they are in the same file; I sometimes prepare my sequences that way when I am aligning genomes with plasmids, or working with draft genomes.
3) Yes, I prefer using genbank files for the reference, as when zoomed in, you will be able to see the annotation for the regions of interest. 4) Mauve should work fine on 64bit Windows as long as you have the Java runtime environment.

Are you running into any particular issues?


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